Usually the option "restore filesystem" from recovery menu fixes most of the problems, i use to initiate it manually incase i have a ftp transfer interrupted
Also incase the games freezes or crashes whille im doing tests modifying some game files, this kind of freezes and crashes could damage the filesystem too
What i mentioned about permanent damage to the filesystem (software) is something i noticed in my PS3 after having a lot of freezes and crashes, and ftp interrupted transfers... there is a point where are cummulated many errors but the PS3 continues working normally most of the time... but eventually the XMB have lag or the xmbingame takes lot of time to load with spinning icons, also some ftp transfers does tiny "pauses" when is writing to the problematic sectors, etc...
Everything is related with a low access speed to the filesystem
Yeah, the hdd of my PS3 needs a format and a surface scan

Im aware that eventually is not going to be able to complete the "restore filesystem" and im going to lost all the hdd contents because is going to force me to format the hdd, but i dont care because i use to backup saves and trophies to PC