Cool as it is to actually see them, leaving fuel tanks and reactors exposed like that is just asking for trouble. That says to Klingons and their ilk "Hit Me Here."
Here's the thing, though, another thing that Trek tends to overlook: A warp bubble is a pretty effective deflector shield. You're bending spacetime around you, so you can send pretty much anything onto a trajectory that misses you altogether. Realistic space combat wouldn't be anything like we're used to on Earth or anything like what's portrayed in onscreen fiction. The distances and velocities would be far greater, for one thing. You wouldn't be close enough to an enemy ship to make out detail; they'd be a distant point of light. And the weapons I've generally seen used in realistic space combat in prose are pretty much all-or-nothing -- if they hit the ship at all, then the entire ship is vaporized, so it doesn't matter if there are exposed areas. In that context, armor would be a useless amount of extra mass. Except, of course, for the armor needed to protect the crew against cosmic radiation and micrometeoroids.