Well if I was desinging a ship, I would place seperate forcefields around these devices for extra protection.
And I know that Starfleets engineer's would come to some type of similar idea to insure that it stays shielded no matter what.
As for the OP, I think that's a great idea, unless the crew kept their personal shielding on, while in the ship, during wartime.
But really, as far as gameplay goes, that idea would be too overpowered. Even though most likely, realistic.
Often times, realism is sacraficed for well balanced gameplay, sto is no diffrent.
It's not that there is a background/lore/technological reason for it, even in canon television/movies.
If you can beam an away team onto the ship as part of a boarding party, then you can beam a steel rod into the brain of people on said ship unless every single crew member had a personal shield. (Ever hear of personal shields mentioned in any of the TV episodes without it being some form of special equipment?) At the very least, you can beam a chunk of matter into the middle of a conduit to screw up ship's systems. It would be silly to state that every single piece of equipment was individually shielded when a team could be beamed into an enclosed space.
Better yet, beam large pockets of air into the middle of the outer hull in multiple places. (For those that argue that one can only beam into very light matter such as air, then fine... beam parts of the enemy hull about 10m further out into space.)
Stuff like that was not done, simply because it would not make for interesting television. (Or perhaps too disturbing, in the case of metal rods to the brain.) You just gotta get the boarding party on board to duke it out in a phaser battle and sabotage systems by hand!