Well, using the FF&S you can certainly make a Rapid Fire Energy weapon, and you can tune it to be as "effective" as you want.
Specifically with TNE, but even AHL and MT, the game is penetration vs armor. If you shoot a round that has a penetration of 10 vs an armor of 20 it's pretty much going to just bounce off. Mind, this doesn't account for, say, hitting the same spot over and over and over.
Also, the TNE mechanic is effectively "Weapon dmg + 2D6 - Target Armor == internal damage". So a Pen: 10 weapon against 20 armor will poke SOME holes, (i.e. when the dice roll an 11 or 12), but not very often.
So, if you want to create an energy gun that can perhaps poke holes or do minor damage, you can build as powerful a gun as you want, and then armor the ships appropriately.
Lasers are notable because they have very high penetration, but don't do a lot of damage.
Finally, making fiction "compatible" with a gaming system is, IMHO, a mistake. It's certainly fair to use something like FF&S to flesh out ships and such, since it's reasonably "realistic", but certainly don't be hamstrung by some rule set in terms of telling your story.