The computer differentiates. Not sure why this is such a leap. The system is able to perfectly rebuild you because it analyzes you as you come in. It needs to know what to rebuild so it scans every part to rebuild. The system is able to tell between a tricorder and a phaser. There is no way for a villain to capitalize on this if they’re the one beaming onto any Starfleet ship because Starfleet is in control.

You could attack the away party and nuke the planet but it makes no sense to do so. Congrats. You’ve killed a couple people from the away team. The only thing you’ve done is guarantee you’ll be hunted down by Starfleet.

The deflector shields prevent ships from ramming ships. The shields prevent matter from entering.

Anti matter is insanely volatile and you’re not going to be able to casually pack the ship full of it

Ships have been used as suicide vessels that let their warp drive go critical. They’ve done this on ships in space as well as entering space stations cloaked and then detonating.

Nah, it is not “fucking stupid”.