My tiny Eagle can nearly take a Corsair gunboat on its own, and thats with someone competent at the wheel. Two fighters should have no problem, if they are flown correctly.
The only limitations to what you can achieve in any craft is your skill.
Missiles are usable, I just find them more trouble than they're worth and leave them alone. There are some people out there who use them to great effect, though.
Also, Gunboats aren't really overpowered, its just battleships and cruisers (cruisers especially so) that are underpowered. I mean, its very hard, but not impossible, to take a battleship alone in a bomber. Of course, you have to be a good pilot, and the battleship captain has to be new in his shiny battleship. However, two bombers have no problems against a battleship, and even a sizable escort has a real problem trying to deal enough damage to the bombers.
Personally, I have one gunboat, and I use missiles on it for stripping guns from any small things, and energy guns for ripping shields and taking capital ships. Missiles, while being completely useless against capital ships, are a godsend against fighters and bombers. Therefore, missiles are usually used if they:
1. Particularly suit the user's style, or
2. Are required in team combat.
The bug you describe seems unfixable unless the radius of all missile explosions increases, and that will just mean complete destruction to any vanilla fighter.
