Yeah, they're difficult to use, but get a constant stream of fire on a fighter it'll lose power and become a sitting duck. Best used in a head on encounter as you're more likely to hit your target as they're more likely to stay on a true path against you as they try and bring their guns to bear. All of a sudden they lose power and bang easy kill. Doesn't last long though, so if you miss them and have to come around for another pass they're most likely to have got system power back again.
The Y-Wing is a good ion cannon ship as with a gunner as it can hit chasing fighters with ion cannon fire and then easily pick them off too.
So in short, tricky to use, but get a good hit and it is a really effective weapon.