Cannons stack right now so people can have more interesting weapons than just 1 kind of gun. The functionality provided by 'stacking' is a precursor to a wider variety of weapons coming down the road, but have not been implemented (remember, weapon overhaul got 3rd place behind ship movement and player movement in the vote).
As soon as there is a sufficient depth in weapons, I can assure you that the days of 'stacking' as we know them will be over. That said, 'stacking' will be first replaced with prefab weapons (the first of which we have already seen). After prefabs have been well defined, work will then begin on making many systems modular and component-driven. This means that the function of the _______ (weapon in this case) will be determined by its component blocks, and not necessarily by a predetermined weapon type. Therefore it will come down to decisions like: if I add this flux reflector damage will be increased by 10%, but power requirements will be increased 25%. Things will be much more complicated but will provide us with the freedom to make a huge variety in weapons (as well as many other important devices like FTL drives and shipboard computers).
Ships are very easy to destroy at the moment because shields have yet to be implemented. They will fundamentally change the game when they are, and gameplay will have to evolve with them.