Dual novas can not drop shields better than a supernova/nova bomber, that's why you don't see them often. Not to mention, you still only get 70 torpedoes, so it's not the most effective loadout. Against hull and turrets, the nova is much more effective than the supernova. More accurate at range too.
Most capital ships I've seen mount full primaries and slap on a mortar. They don't use missiles because they don't understand that they are tactical use weapons. (approximately) 85% of battleships I've seen simply mount full primaries, a heavy mortar and expect to beat everything. They may beat other battleships and cruisers by brute force (and by cruising up to them), but they don't stand a chance against bombers. Strangely enough, ones with solaris... actually do stand a chance. I've seen two Legates effectively use solaris to fend off bombers. Another example is an Osiris with flak and solaris - its a very dangerous enemy as a bomber, as you can't get close and it's hard to hit it from a distance.
Most capital ship pilots I say simply use turrets and mortars, because they are simple. Missiles require timing and proper targetting to be effective. Primaries just require the pilot to hold down the mouse button.
The same issue occurs with bombers - the supernova is a simpler weapon to use than the nova torpedo. Novas require timing and aiming, while the supernova isn't as complicated.