I'm am very happy to see this disaster of data organization in NWN2 being addressed. Fortunately, the solution should be easier to implement than what is already there.
For .mods. Really, they should contain all the localized resources used by the module and SPECIFIED by the module designer, IN ONE CONVENIENT PLACE <----most important thing. A .mod should be an archive of files and directories to keep things separate from other .mods and for easy transport and management. Thus, EVERYTHING is managed through the .mod. It is the ROOT of all resources, if you will. This makes the most sense.
Please, lets not have a .mod and THEN have directories for haks and tlks OUTSIDE the .mod that the .mod depends on. This is where things are now and it its too confusing. Sharing common haks between mods is far far less of a concern than compact, self-contained management because disk space is far more abundant and the server can be made to not redundantly load resources (by using their crc hash or unique id).
The simplest solution is always the best. Put everything into the .mod and for that matter most of the bigger PW's and modules will use directory mode anyway. All their custom content, regular content, and myriad resources can then be managed under one tree. This allows for convenient use of other tools like version control FOR ALL RESOURCES.
A simple CRC checksum of sorts between the server and the client can detect any tampering. Easy.
The override folder stays as is.
I've abandoned my NWN2 endeavors for the past 5 months because of this headache. So hopefully it can be fixed.