Ahh. I thought the data directory limit might have been in reference to total files contained. I have 343 files and 16 directories with about 10 more esp's on the docket.
As an FYI, data directory limit for me is *exactly* 400 ESP + ESM + BSA files. No other files matter.
If I add those up and they are 400 or > then after playing just a few minutes I will see missing landscape, meshes/textures dissapear, AI goes wonkey, sky turns purple and/or the game crashes shortly afterwards.
If I remove one ESP or ESM or BSA file, so I am at 399, then everything works fine. Doesn't matter which one. Big, small, complex, simple... its purely the total count. I merge many mods BSA files together using OBMM to work around this.
This is all discussed in another thread, search for "thrashing" or something like that.