Well…
The HC 201 has 12% key bonus and two extra mission slots (8) compared to the HC 101 (6)
The HC 301 has two satellite slots and 6% key bonus and 10 mission slots
The Muller 400 has an even smaller hitbox compared to the M404 along with 14 mission slots
The M408 has two engines and two extra mission slots (18) compared to the M404’s 16
And then there’s the BX family, all of them have dual pylons but each iteration has different power caps.
The BX-6 has the smallest hitbox out of all the bombers and is the fastest among them but it is limited to 
7 for each pylon at fp 14 though you can get 8 pylons at fp 24. 17 mission slots
The BX-7 has a front facing satellite slot and can have more firepower compared to the BX-6 at 8 for each pylon at fp 16 and two 9 pylons at fp 26. 18 mission slots
The BX-8 has two 9 pylons at fp 18 and you can get two 10 pylons at fp 28. It’s also equipped with 4 satellite slots and 19 mission slots.
The BX-9 has five satellite slots, and it’s the most powerful bomber with 10 on each pylon at fp 20 and at fp 30, you get two 11 pylons, although the only weapons that takes advantage of it are Boron Railgun and Absolver Beam since Boron has 13 power levels and Absolver has 21 power levels instead of 12 for every other weapon.