Maybe check in /dev_hdd0/game folder if you have _INST_* or _DEL_* folders.
These folders could remain consuming a lot of hdd space, if the console hanged or was shutdown during a game installation or deletion.
multiMAN (BLES80608) and IRISMAN00 cache folders are another places that may consume a lot of space.
These folders are obsolete nowadays, but these backup managers still support *.666** and make a copy of the large files (+4GB) in these folder when the games are copied to/from USB FAT32.
Another place that could consume a lot of space is /dev_hdd0/home, specially when the user have installed or played many games with trophies or savedata, or created several users.
A rebuild database could help to discover some games that remain installed, but not appear on XMB. Just be aware that rebuilding the database the configuration of "albums" for games in XMB will be lost.
Also check the folders for content of backup managers: GAMES, GAMEZ, PS3ISO, PS2ISO, PSXISO, PSPISO, ROMS, Packages, or /dev_hdd0/tmp/wmtmp
If the above doesn't help, I suggest to backup your important data and reset the console to factory settings and format the hdd. This could take you several hours to do it.