That's very true, and bomber starships are actually pretty fragile in general. Unlock mk1 Cloaker starships, which will provide anti-sniper protection and another level of general protection to your bomber starships, and use them independently of your fleet.
Definitely learn how to manipulate multiple control groups of disparate ships at once, you'll become much more efficient. When it comes to fleet ships, I'll usually split them by speed groups and assign starships that way. 68-100 or so is the fighters, bombers, FF bearers, grenade launchers, the "fast attack heavy hitting" group. Cloakers will not go in this blob, since their role is different. Slower ships like Missile Frigates, Beam Frigates, and MLRS will go in a different blob, supported by the Fleet Starships to provide some artillery support with munitions boosting. That's just an example, mess around and find something that works for you!