In my little newbie experience so far (so feel free to ignore my input ^^), the Siege S. is better than the Bomber S., but saying i have tried every strategy with both ships would be a lie
Even with 2x Health and 15x Armor Bomber S. dies 10x faster than Siege in destroying non mobile threats (playing against 2x AI-7 Zenith Descendants at the moment). In this case 38k range defeats increased Health+Armor+Speed in survivability at least, Bomber S. having to get real close to the target.
In a non micro way, group moving them with you fleet is a complete waste of their great speed, so it would seem to me they need a bit of micro to take advantage of them.
If i decide to raid an enemy system next to mine to get rid of some specific structure, i think Siege would still be better, at least (unless they are heavily Anti-Artillery, but I didn't try this enough to reach any kind of definitive conclusion). PS: AT least, again, in survivability, still don't know who would get the faster kill, taking in acount SS has a Cap. of 5 BB 4.
Siege S. can also safely start pounding on enemy Force Fields while my main force gets rid of the immediate mobile threats.
Siege has 5000 Engine Damage Bonus compared to Bomber, not yet sure it makes a huge difference.
Bomber S. has great speed that allows rapid intervention in case of "oh crap an enemy biggy is chewing the health of my command center at an alarming rate 4 hops from where i am!"
And as a matter of resource cost, a ship that has a higher survivability is cheaper than a ship that costs the same and dies often (costs of both ships are mirrored I know SS being 4k/60k vs 60k/4k for BS ).
Bomber Starships don't need research unlock (interesting question would be, would you research them if they were initially locked?) so I'll continue to make them if I'm not short on resources, but I will still always build Siege Starships first.
Will be testing some more.