In the EMP universe, almost all ships use one form of energy shielding or another; either in the form of intraarmor projectors, or surface/bubble shielding. The introduction of shield technology actually dramatically changed combat doctrine; prior engagements usually involved large numbers of single-person craft that would engage in high speed "jousting", since even strikecraft could mount one-hit-kill weapons. This of course made freighter escort missions utter hell :-p.
As far as weaponry is concerned, the terran faction tends to use a combination of large railguns, plasma beams, and plasma projectile weaponry. Ammunition storage for railguns is concentrated near the core of ships, and storage for plasma weapons is generally minimal, since source mass can be compressed into ultradense solids.
Military ships use Hydrogen/AM reactors, which is also used as reaction mass by engines. Due to the volatility of the fuel, reactor blocks are heavily shielded, and the fuel storage itself is concentrated in the rear (uncrewed) core of ships. The hydrogen is usually skimmed off of gas giants, and antihydrogen is generated at particle accelerator centers occupying inner orbits near stars.
But yeah, I usually try to think about the internal mechanics of ships when designing them, though not to the point of insanity.