If ion cannon are to be implemented, then you should get points for using them. Otherwise the stats freaks won't go anywhere near them.
The big mystery in my eyes is how ion cannons work. In the X-Wing series, they do normal damage to shields and then massive damage to "SYS%" integrity. When this reaches 0%, the ship is completely immobilized. Then in the Rogue Squadron series, they penetrate shields and do even more massive damage to ships' systems. But considering how woefully inaccurate the series is about nearly everything, I'd rather take that as a sign ion cannons don't work that way. In addition, the stupid "huge orb of light that needs an eternity to recharge"-approach is beyond silly - ion cannons are fired like lasers.
I say go with the X-Wing series' approach. Either way, you should have to reduce a ship's shields, if it has them, to zero before you can do any sort of damage.
"One of the bitches actually gave birth while she was attacking, and her puppies joined in on the carnage."
--the awesomeness that is Boatmurdered.