Hi Adam, welcome to the FlexHub forum!
The hub itself doesn't download filelists and there's no bot that can be added on the serverside, FlexHub doesn't have a Lua API yet to add scripts yourself. There probably are clientside scripts (that can run in your DC client) that can take care of downloading filelists and scan them for certain content, but I don't have experience with them. You could also use ADL search to help with that, you can create automated actions for certain matches in a filelist. But they tend to generate false positives also, so be careful trying to fully automate it.
To allow only registered users to download use:
!set unregged_download false
When a user selfregisters, he will have the profile 'Reg', you can see the profile with !showprofile reg and you can specify the rights for that profile with the allow and override commands. Use !allow -h or !override -h for help with those commands, or check the manual. There's also the !modprofile command for some extra profile settings.
With those commands you can also modify the profile that admins use.