To the propagators of long range torpedo bomber (TB) ships:
For those who are fans of Star Trek, there is something called the Picard maneuver. Basically, a ship uses hyperdrive to jump right on top, or really close to, its target. That way, a loaded beam ship(BS) can tear apart a TB in a very short time, wasting minimum fuel for a chase (fuel usage is smaller for jumping than sprinting such a distance, since it is a time-based consumption dependency). Note: I do agree that the accuracy for such jumps is limited and think, that there should be tech modifications for these options.
Then again, you MIGHT be able to design a BS with faster engines and
>= firepower than a similar TB, taking some damage and then outgunning the TB at point blank range.
The third solution is in the area of maneuver strategy. A ship runs from the TB, then turns around (greater turning engines, a hint) and is right within range before the TB can turn and stays there at least some time.
So, these ideas could be implemented as AI strategic construction variations, and for the rest of us it becomes evident that in this marvelous game the sky's the limit for our (and the devs') inventiveness.