3000 subfolders… that sounds already like a mess.
I organise my music by genre. So I have maybe about 40-60 folders max (including sub genres)
Every track I added there is named in the same way (artist - track name (mix/remix/edit))
Every operating system lets You sort by the date of creation of the file.
So if I want to look up a track from a specific year and genre - I am able to find it without any database software.
Then in Engine I keep clean my tags and track info etc…
This makes search fast, easy and accurate.
So maintenance of Your data base starts from a single file and a general idea of how You want to be able to find it and manage that music library later on between multiple platforms (example traktor, engine, serato, rekordbox…)