On the one hand I could see it being very useful, fast responce and reports for ship wide problems, but on the other he is connected to systems that could be taking damage.
In an old fic of mine I had the main computer represented as a holographic avatar as a character, made for interesting story ideas for problems with the computer but brought up the idea that damage to the computer or ship could cause "pain" to the program.
An actual flesh and blood 'person' hooked up to the computer could have all sorts of unforseen dangers, hacking, brain damage, the fact that the computer is on 24/7, so is he as well? etc
In an old fic of mine I had the main computer represented as a holographic avatar as a character, made for interesting story ideas for problems with the computer but brought up the idea that damage to the computer or ship could cause "pain" to the program.
An actual flesh and blood 'person' hooked up to the computer could have all sorts of unforseen dangers, hacking, brain damage, the fact that the computer is on 24/7, so is he as well? etc