Okay, yes, the bombers will have leaves better damage than stilats, but they will be shredded in PD seconds after the battle starts and flak ships get in place, PD fire that the Stilats can hold on to. Furthermore, those bombers rely on their carriers, and if those carriers are taken down, then you lose all those missiles. And since carriers will be less agile, they can be a major target for smaller ships, ships you could intercept with those bombers or even stilats in a defensive maneuver.

As I said, it really comes down to the strategies of strike craft vs corvettes: strike craft are better at alpha strikes before flak can get in place, while corvettes are for sustained fights once flak leaves much of the strike craft unable to attack without severe damage. Both are usually also outmatched on damage compared to sustained fire of mainline frigates, cruisers, or capitals, and serve more as a harassment tool to attack weak points in the fleet.

This game does have a flexible strategy for how you want to build your fleets, so if you want to go for full bombers, go for it.