Well, what is in your misc folder? Is there enough of any one type to warrant its own high-level folder? If not, don't worry about it.
But if you want to see other people's setups, mine is:
sampler instruments: all kontakt, sfz, decent sampler, etc.. May have loose samples but intended to load an instrument in the respective sampler. locked samplers usually have their own top-level folder (e.g, EastWest, UVI Soundbanks). I keep them in this folder since I can search just that for WAV/etc. files.
samples: loose assets, no files in this level
- fx: sound fx including foley and designed, that I can point metadata-based categorization tools like Basehead and Soundminer at. I can also feed this into Sononym.
- instruments: My favorite loose samples I can throw into a synth, sampler, or granulizer. I am using symlinks to avoid duplication since I am drawing these from my sampler instruments folder and other places (e.g., product assets).
- IR: with subfolders for creation tools (e.g., Dirac impulse), guitar (cabs), devices, mics, resonant bodies, algo reverbs, plates, spring, real spaces, product IRs, creative. Under creative I symlink my favorite non-IR samples that make good creative IRs. Under product IRs I extract or symlink IRs from various products like Kontakt instruments, Waves WIR, etc..
- loops: BPM sync with metadata, lots of rx2
- metronome: metronome samples for DAW
- MIDI: drum patterns (groove extraction), classical, chord progs, arp patterns. Melodic I can use direct or throw into Cthulhu and other tools.
- packs: samples packs by developer, then subfolder for each product. Each product is tagged in the folder name, usually genre/type (e.g., Samples From Mars/808 [Machine], That Sound/1985 [Acoustic, Synthwave]). This helps me filter in other tools. This also helps with licensing as licensing details are in the product folder. All sample packs go to an incoming resources folder first, where I will delete garbage and reorganize/metatag to my spec. I have a backlog from before I started doing this and am slowly whittling it away.
- tools: anechoic samples, scientific, test signals, test files
- tunings: scala files
- vocals: BPM sync. chopping, granular fodder.
- waveforms: single cycle
- wavetables: mostly mine and other Serum-compatible 2048 WAVs I can throw into many synths, a handful I've converted for hardware (e.g., MicroMonsta).
I used to have my sample packs broken up by type (e.g., kick, snare) but that was an ID and licensing nightmare. Much easier now with tools like XO. I tried Atlas but its categorization is relatively useless as others have attested. No one tool is best. Use a combination that suits your workflow.
For my incoming resources, I find Resonic Pro to be fastest. It's file-oriented just like how incoming sample packs usually are, and it can show what kind of metadata it has. The free version is enough for file management but Pro adds more metadata access and I can extract sections of samples. So it's great for trimming or grabbing the interesting parts only. I can create/delete folders, move files around. It can use Explorer menu so I can convert formats (third party tool), edit metadata (third party tool), etc.. Resonic lets me re-organize how I want before ingestion. Unfortunately Windows only and no idea what if any is available on the Mac.
For intentional discovery of drum-like samples nothing beats XO. Its categorization is better than anything else. You'll notice I already discussed orienting my library to suit it. The filtering is awesome. You don't necessarily need multiple maps if you leverage this. Like I said, product folders get tagged. So I can filter for "acoustic clap" and click "clap" and find organic layers to throw under a drum machine snare and audition them in context of the song as the sequence is playing. I also did the additional step of adding developers at the top level instead of giving it my top-level sample folder. So I can include/exclude developers easily and it rescans at the developer level when I make changes.
In terms of skipping over due to density there are two main solutions. Zoom in or use the Similarity bar on the bottom. Once you understand how the map is laid out the workflow is blazingly fast. Generally timbre is dark from left and brighter to right, and body longer from bottom and snappier to top per color/type. Find a sound close enough to what's in your head then zoom in and draw a path you can backtrack, or use the Similarity bar to hone in on your current selection.
I'm not using XO as a drum machine, it's not meant to be one. The sequencing is there to build your kit in situ (or export loops). If you're sequencing a whole song, it really helps to have a drum rack/machine to export and drag the samples into. The export panel is so good. Get them raw or processed, single sample or the whole rack, the pattern raw or processed, the beat as MIDI, normalized or not. So I can drag the kit into say, Battery, do further layering and processing, and save the kit into the project folder for backup. I do my drum programming in DAW and sequencing with other tools. If your workflow is different but you prioritize discovery, you could use XO for that and throw the kit you built into whatever sequencing tool you use.
I use my DAW's native browser for loops (REAPER Media Explorer databased). I can search by folder, file name, metadata like BPM. I use Sononym for search and discovery. It can find the needle in the haystack via musically and sonically meaningful properties. Development has been slow but it's been consistent and incremental lately. They added really nice features recently, and there's a public roadmap you can get involved in that is promising. Nothing else as good as its Duplicate Finder. Its categorization is not perfect but it's as good as it gets right now, and you can reassign en-masse. Yes, you can (mass) rename files using tokens for anything it knows about the file including metadata and detected key. I've been using this with Resonic to do the up-front organization necessary to make other tools work better for me.
If you're working in post or using field recordings then tools like Soundminer/Basehead/etc. are. since they're description metadata-based and the good devs like Boom categorize it for you. But they're expecting you to have post-like budgets. Though BaseHead recently released a free "Creator Edition" which looks sufficient for musical and social media use (69k asset limit): https://baseheadinc.com/creator/
For music, we were largely left to ourselves but now have these tools that can automatically categorize them in terms we use. Also helps to stick with devs that do the metadata for you and avoid the lazy devs who don't tag/name/organize/trim to black.
As for lots of samples and tools getting bogged down. Sononym does deep analysis on new files but as long as you don't do a hard refresh it's reasonable. The initial analysis can take some time. But it's using SQLite which is as fast as possible on a local file system. It does leave database files in the root of the relevant folder which can get large, but that means you have a lot of samples so you clearly have the room for it. Really helps to have the databases on an SSD, and there are symlink guides on the Sononym website.
XO uses SQLite too, and scanning for changes happens in the background until you explicitly scan & refresh where it will analyze and update. Initial scan can take some time. Went overnight for me, but I had 30 GB which is likely atypical. That's why I'm going back doing QC on them, and being strict on re-ingest. A lot of garbage and I'm sure I can whittle that down to a third if not more; I'm already down to 20 GB and just getting started.
The cool thing about SQlite is if you have an appropriate tool (e.g., sqlite studio) you can open up the databases and search via SQL query. For example, use the data in XO to rename files programmatically with scripting.