I don't know if Cruisers can take Fighters. The fighters might not be able to do much damage to a cruiser, but that's different than a cruiser being effective against a fighter.
Anyways, what about using Novas against gunboats? 10,000 less energy use, faster refire, the possibility of destroying the gunboat's turrets, the ability to fire the bomber's guns while also shooting the torpedo, all add up to effectiveness.
Personally, the only downside to using Novas for me is the ammo. But it needs a downside, I suppose, if it's got better refire, energy usage, and damage compared to a snac.