file systems on HDD do get corrupted with time.
I recently had to repair my 1Tb elements drive, it would not create the index for the media server and sometimes a minutes before a file would start to play but that was all. Everything actually played fine. I connected it to my PC and windows took forever analysing it and found numerous errors the the file system structure. After repair and analysing again all seems OK.
If you have the opportunity to reformat it may help, or not, its up to you
you asked "all" about organising files, I have over 700 video files (my 10,000+ music files are now on a NAS) sorted in folders 4 deep and have never noticed any problems with organising them in that way.