sam.log and samygo.log exist in /mnt/
deactivated "apps" - for sure they are just scripts - /mnt/etc/init.d/
I think deleting is absolete - except logs, rest files are small and does not require a lot of space. Removing it you don`t get any signifficant improvement nor more storage space.
However factory reset + Smarthub reset should do the job in all cases.