I recently reinstalled NWN Diamond Edition to play some custom modules but the modules and hak folders are missing.
I tried creating the folders but the modules still didn't show up.
I tried using the toolset to see if it would path to where the modules are stored, but pressing save or load freezes the application.
Note this is Diamond Edition, not Beamdog's Enhanced Edition.

Found it.
If anyone is searching and wants to know, I reinstalled it using GoG Galaxy, right clicked on the game and went to game folder through there.

In Diamond Edition the mod and hak folders should be found directly within the game folder (following your individual installation path). In Enhanced Edition, these folders are created in user/documents/ instead.

Same goes for the savegames and everything else, but I once had to find out that GOG's Diamond and Enhanced Edition installations were using the same save folder location in user/documents, which is subpar, and the reason was that GOG had changed the paths in one of the .ini files of the Diamond Edition, I think it was nwn.ini.

So I suspect, in your case something similar might have been the cause. What folder did Galaxy point you to?