Just because you lost the comm doesn't mean you've lost weapons control. Heck, the movie "Crimson Tide" is all about the loss of communications but not weapons.
Communications with HQ weren't hardwired; communications with the onboard SLBMs were. Any communications between command crew members would of course be fully internal and hardwired, and probably far less vulnerable to damage than, say, warp engines or life support. Or the crew, for that matter. If you
can take down comms, the entire ship is your oyster (without the annoying hard shell)...
Well, ID hinted that Chekov had been apprenticing with Scotty, so there is the possibility that he was being trained to be the number two officer.
It might also be considered that if Scotty walked out, then anybody trained by him would be a risk factor as well. Better bypass the obvious choices, then, and appoint a junior yes-man Kirk could count on.
groups that are communicating purely through data streams is something will many humans would struggle with.
In TNG, and probably in ENT already, those data streams could carry the whole range of human interaction, though. Instead of just text messages, an officer could send text, graphics, sound, his face, his body, his body temperature and his odors if need be. And every user could scale this virtual reality to match her personal needs (something she couldn't do in physical interaction where turning off sounds, involuntary gestures or body odors would require so much technology it would amount to virtual reality anyway).
It wouldn't be a struggle for our heroes, who would have grown up with such technology and the associated user culture. But it would be a struggle for the audience - which is why something like that will for the time being only be seen in individual scifi movies, not in long-running television shows.
Timo Saloniemi