They also keep their firearms in safes (or weapon lockers, where/if available), along with any related ammo. Which is where the gripe comes in, as there's no way a long-sealed military base would be stocked with jury-rigged post-war weaponry.
There's also the fact that, contrary to the game-play necessity of uniformity in the lock-picking mini-game, safe-cracking requires specialized tools and knowledge if you want the contents to still be intact once you've finally breached the door. Even then you've generally rendered it useless as a safe from then on, since the door tends to be irreparably compromised. Since the seals on safes are still intact (which I'll grant is another deference to game-play necessity), it only makes sense that the contents, including any weapons and/or armor, would be prewar in origin.
Basically, what is being asked is that some common sense be applied when generating loot lists for sealed containers. Note that this also applies to the difficulty of the lock/locking mechanism, as there's very little more annoying than cracking a Master lock and, instead of the top-tier loot normally associated with such security, finding 3 10mm rounds and a can of Cram.