Is this why visuals will occasionally sttuter?

Unlikely. The only real benefit that the new directory layout gives is in database rebuilds, and we've not actually got around to measuring it, so it might not be much.

A large number of FIDs will cause directory indexes to be slower, but since the player has (usually) already pre-cached parts of the next few tracks asynchronously, a stutter would be unlikely to result.

Also, if this was causing the visuals to stutter, the music playback would stutter also. This could happen when memory gets low, which can happen if you've got a lot of tracks -- the database and the cache share the same space.

More likely is that you're (very occasionally) borderline on CPU usage, and the visuals are getting starved.