bombers are basically immune to fortresses. One thing I maybe could recommend is the use of warheads - you have three choices, with varying results and AIP:
EMP warhead - Kinda nice, makes everything quiet so you can do random things. Planet-wide effect, 30s or so per
Lightning warhead - blows up small ships first, good at clearing tons of junk, not so great against fortresses
Armored warhead - super great at blowing up fortress, marginally less useful against masses of units (lower range is mostly the thing).
Either of these will really help if you absolute *must* have it. Otherwise, consider waves of suicide bombers to blow up the fortress - A fortress basically cannot destroy bombers. (or any polycrystal hull). itll be timely and kinda expensive, but eventually the fort will die.
Final option is just to ignore it. A fort's range is actually kinda small , so you can blow up what you need and take the command station and then put up your own, getting the ars and other things.