So, I'm not actually worried here about exceeding skyrim's maximum limit for ESPs, which I understand to be 255.

However, I seem to remember that in years past there was some hubbub suggesting that having too many files of any kind in your top level skryim/data/ folder would cause issues.

Was this an unsubstantiated guess that became a rumor and was later proven false, something that Bethesda fixed, or something I need to worry about? The vast majority of the mods I have installed have BSAs, which I understand is considered the best and safest practice nowadays.

Technically, the limit is 256. However, Skyrim.esm, Update.esm, and your saved game are included in the total. Leaving you with 253 esm or esp you can add.

I recall the issue you are asking about, however I do not know what was proven or not. I do know that ShadeMe released http://skyrim.nexusmods.com/mods/19556/? to address something along these lines.

To me, that's proof enough that there is something to the question.

Thanks for that! If what the Nitpick page says is accurate then it's only a matter of total ESP/ESMs over 508, and I don't have several hundred inactive game files. But I'll install that just in case, looks like a useful little mod.

It is always a good idea to have a tidy Data Files folder. The only files in there should be for active mods or ones normally active.

This is the main reason why Mod Organizer is so great. It keeps the Data folder completely clean which means there is really no need for a re-install of Skyrim whatsoever.

Now if only there was a way to keep ENB files out of the root folder, then I would never ever open up the Skyrim folder ever again.