I recently had a hardware failure and ended up reinstalling the current version (ZS 3.9.3 with 64-bit kernel 4.14.83). Even though I restored the configuration from a backup, the nDPI tables were now present. So, I think the original problem must have been due to some historical upgrade that messed it up.
If you need this functionality, I would backup your running configuration, reinstall ZS and restore the configuration. That should make it work.