Not all ships carry weapons or are willing or able to shoot back. Stasis webification tech and warp-disruptor tech can immobilize an enemy ship enough that opening your own hatch to send off a few dozen or hundred troopers in suits to blow open a hatch on the opposing hull and make their entry is not impossible. While this is not present in-game as a mechanic (it might just make piracy and anti-piracy a bit more interesting in the few situations that don't include blobbery, as one example) Lyn's example shows it's been considered from a PF stand-point and quite frankly, the possibility is a very logical one to assume - the opposing side don't have to be a ship - a fleet might go bust an enemy dead-space location for instance and instead of destroying it (valuable people/stuff inside or whatever) they make a hole due to the structure being to small to dock in, and send in troops to assume control and capture the place.
It could make missions more interesting. "Please take with you these two platoons of marines and go capture the dead-space facility in location X of system Y, we have great reason to think they work for Z secretly and want proof and prisoners for interrogation, so we need them alive, don't destroy the facility. "
Many possibilities here really, and I'm convinced the only reason we don't see ship/station/complex boarding actions is solely due to game-mechanics, and IIRC there is little to flesh this part of the game out, besides small things like the piece Lyn quoted.