Star Trek also has teleporters, androids, and magical deflector dishes capable of solving every known problem in the universe (Voyager).
For starters, Star Trek isn't exactly the height of realism, converting 1 person into energy means you have enough energy to blow up a planet, much less some puny little spaceship - don't bother with the dampening buffer explanation, its not very convincing.
If you want to take it one step further, the Defiant isn't a fighter. Putting cloaking devices on a cruiser-sized vessel is a wee bit different from putting such a device on a fighter, where the cloaking device would be about half the size of the fighter. Capital ships in Star Trek obviously have room to spare, they always have nearly empty cargo bays.
Finally, Freespace2 isn't Star Trek. The plot is different, the tech is different, you can't use what's in one to justify what you do to the other.
Just my 2 cents