You know, I just got done ranting in another thread about how I like for Trek to make sense, BUT, there IS a certain amount of handwaving, ala the old Marvel No-Prizes, that has to be done with some of this stuff.
Because really if you get down to it, with advanced AIs that are indistinguishable from living beings on the holodeck, and speed of light drives and weapons like phasers, any ship(s) to ship(s) battle would come down to who made the decision to engage in combat first, and then whose computers, weapons, and defenses were faster. The organics on board, especially if they weren't the aggressors, might only know that something happened because the computer reports that it did, or because they are captured or in a broken ship waiting to be captured, killed, rescued, or die when they run out of breathable atmo. The reason I say that is because while WE might not automate our systems to attack, some species out of all of those out there would, and then the rest would have no choice but to automate response systems, and maybe even to automate ATTACK systems triggered by sensor recognition of a hostile above a certain percentage of accuracy.
So, obviously there's some reason that isn't true that we haven't been told, and obviously there's a reason for some of the rest of this that we just haven't been told, too.