As in many sci-fi games/movies/whatever, I think the term "plasma weapon" can apply to most, if not all, lasery weapons. Terran Huge Turrets, Shivan Megafunks, beam cannons, Lucifer cannons, and all other energy-based weapons can simply be called "plasma weapons".
The OP is wondering whether the Shivans use subspace weapon mechanisms all the time because apparently, he says that the same firing effects were seen in both the Shivan firing that "integrated plasma weapon" and when the Manticore fired a missile at a Herc in the FS2 cutscene.
But really, I think there's no need to be suspicious of this mysteriously frequent charge-up effect. It's just a flashy...charge-up, to make things more dramatic. Also, notice that if that charge-up were indeed some kind of subspace manipulation mechanism, then the Sathanases should have used it too. But no. Clearly, the Sath fleet in the FS2 ending cutscene didn't charge up their subspace weapons with that flashy effect again.
Finally, as karajorma said, I really think that the weapon the Shivan used in the Taranis cutscene is a beam weapon. Both capital ship beam weapons and the Shivan had a multi-second, expanding ball of light before releasing a vaporizing beam of energy. So yeah, it's most probably a beam weapon.
