I absolutely hate to spend knowledge on anything else than mobile combat equipment, and even then... So the idea of paying knowledge for specific modules seems to be a good way to restrain optimizers like me.
Imo a modular technology should cost 250, maximum 500 knowledge points. I pay 250 for a warp detector, say, which to me is only of real use in the early game.
Some basic modules should be free, but the real powerful modules should cost you. Some modules could be linked to existing turret technology, some chould be unique to the Riot ships (or other, future module ships).
Perhaps this linking to existing techs will also make it possible to upgrade your modules as you unlock higher technologies? Or perhaps this will be the real difference between mark I, II and III - each mark being restrained to technology at its own level?