I'll admit I find your idea intriguing, but it doesn't seem like it could fit my current concept very well.
In a "sandbox" game, it would fit (and would even bridge efficiently with my energy system) allowing any ship to become anything.
My concept revolves around hull types that are much more restrictive. I really want to build the lore/feel/gameplay around these specific hulls.
Each faction have few hulls which they can customize a bit, but not too much as to derail them from their original purpose: a science ship can't be turned into a missile frigate, etc.
Each of these hulls should contribute to the overall strengths and weaknesses of their faction and cover some of the basic roles (leave some opened) etc.
As a result, being able to field any amount of weapons on any ship would be too customizable, and though interesting as a system, it wouldn't support the current design I have in place.
To be in-line with my current approach, not only do I need to have specific slots in place, but ideally, these slots should not only be labeled as "weapon", but rather, as a class of weapon I can use in this slot (energy-powered weapons such as beams, for example, would only theoretically require an energy port, whereas missile launchers would require some form of "door" to the inner cargo rooms of the ship and only minimal power). Since each weapon type plays a much different role, I need to limit the amount of customization a player can make to the core craft's functionality without making it too hermetic...