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.
The tanks and stuff there are really just a placeholder for now, I'll be building new ones. I'll put some covers over sensitive parts, but I think I'll leave them mostly exposed.
Haven't really thought of combat much yet, but I figure any part of the ship that gets hit with any kind of large weapon is going to destroy the whole thing. Lasers, might be pretty survivable though.
All I was going to equip the ship with was some high powered lasers, anyway. Maybe a railgun? I really didn't want to have missiles on here anywhere.
Shuttlecraft? Either have the "garage" enclosure we saw in the show, or have the craft docked directly to the hull and you would enter through an airlock.
I've been thinking about that... I like the idea of the shuttles being docked outside, and not inside. I'm trying to think of a good place to stick them.