Way I see it there are a lot of factors. First off, the amount of firepower your under. Exacty how strong are the beam cannons of FS2? I know that the Enterprise-E's type12 phasers are in the terrawatt range, so are the beam cannons on B5's Whitestars. The turbo lasers on an ISD are each in the Gigawatt range.
Second, the defences of the ship being attacked. The caps in FS2 dont even have shields. Some of 'em dont even have that much armor. Also some ships/stations have the largest concentration of shields and fire around the bridge/command center.
Third, the design of the ship. A big bulky ship is less likely to break apart than one like the 2 Enterprises Kirk captained.
Fourth, some ships have bridges for the benefit of the command crew. A ship with an AI can be run with or without a bridge or even if the command crew is dead.
Still.. when gaming its great to see chunks of metal being blasted all over the place as your guns rip into a ship.

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"It's nearly impossible to defend against an assassin who's willing to die for his cause."
"Agreed. There's only one way to deal with terrorists... locate their base of operations... and destroy them."
"I
love that answer, Captain Hunt." Tyr Anazasi to Dylan Hunt-
Andromeda