im also strongly in favour of generally modular or at least changeable/modifyable weapons.
ideally we'd have something similar to from the depths where the weaponry is built from blocks as well and is dependent on how one builds it
hopefully with the position of elements influencing the characteristics of the weaponry instead/on top of FTD's "connect it all up in any way" which is mostly volume dependent.
for things too small (or maybe instead of the block based model) something like my buddy Flatfingers describes in these two blog entries
http://flatfingers-theory.blogspot.co.at/2009/03/engineering-crafting-modes-in-star-trek.html
http://flatfingers-theory.blogspot.co.at/2009/03/engineering-crafting-modes-in-star-trek_26.html
((ignore the star trek theme, its just the part mechanics im thinking off))
could be used.
with weaponry (and general equipment) being built out of a couple of elements which the player can tweak and swap out to build a better/different version of the equipment.
flatfingers modular approach would (in contrast to the FTD approach) also remove weaponry from the ship itself and make it independent modules one can mount and swap out if desired