I've said this before elsewhere, but I like to place my opinions in the currently active threads.
I suggest that:
All weapons use ammo. Cannons need a photon matrix, Beams need refraction crystals, Missiles need thermal-cores, and Pulse needs kenetic-resonators. The more damage a weapon does, the more ammo it consumers per shot. More thermal cores makes a more explosive missile, and more refraction crystals focus more light into the beam, etc.
All effect modules also need ammo. Ion clouds, kinetic dampeners/amplifiers, overclock modules, etc. which are consumed according to the size of the effect module system.
It is sci-fi, so we can make up cool sounding names for these things even if they don't really make sense, right?
Any effect module that runs out of ammo stops functioning. Passive effect modules either consume ammo over time or when used, depending on what they do. Any weapon that runs out of ammo stops working. Ammo containers can't be shared by weapon systems. So if the big missile system runs out of charges, it cannot borrow ammo from the small missile system directly - you have to use logic systems to move the ammo to the correct containers. Blindly firing is now no longer a good idea, meaning that there is now more benefit to having small and agile ships.
Resource management like this adds siege options to a game. A station and capital ship will eventually run out of ammo, making it a prime target for smaller ships. If you dodge long enough, you will have the advantage. If you cripple supply lines, you will eventually cripple combat ability (even for ships already constructed).
This can also be used in the discussion of immovable station vs. mobile station. If ammo counts are a thing to consider, and ammo can be crafted in factories, but factories don't work on moving ships, then a station has a huge tactical advantage when defending itself which might make up for the station's inability to dodge.
Of course, we have to decide if there will be a basic weapon that rely's on energy rather than ammo, for those few situations where you are completely out.