Some modern military ships are built to Civilian Standards (which is a very complicated thing that I really don't totally understand)
My understanding...well first of all my understanding comes from, say, 20% from disparate sources with the remainder from the essay Ryan posted, so....
Military standard can apparently mean a few things. Like you said, thin plating, closely-spaced frames to allow the ship to "flex" over a shockwave from say a near-miss torpedo or (more intended) a nuclear blast. This also apparently doesn't necessarily mean a longer or shorter service life (many ships built to this standard have been serving a long time, apparently). Military standard also apparently dictates things like watertight door placement and how many you have - for example, on a civilian ferry, you probably have whatever # of watertight doors you legally require and they may or may not be mechanically or hydraulically actuated. On a military vessel,
every hatch inside the hull is a watertight door (hence all the hatches being dogged and stepped) and they're all typically manually actuated since otherwise would be impractical, the expectation being that the crew will latch them as they evacuate the room. This also means that every single room inside the hull is its own individual watertight compartment.
Civilian/military standard also has as much to do with things other than the physical construction of the hull. From what Ryan says, apparently civilian construction can in some cases be more collision and even battle-resistant than military standards, but at the price of losing that flexibility (that was a big concern in the Cold War). Also, your wiring standards can be different and let's say, less battle resistant. Also, shipbuilders and ship procurers, not being idiots, are well aware of all of these advantages and disadvantages and can mix-and-match different standards and requirements to better serve the ship's mission.
Yeah there is that, but it is my understanding there is a lot more there that I just don't know about, hence my comment.