User blog comment:Le Rottweiler/Who’s leaving all this crap lying around‽/@comment-1496755-20150721101837

Equipment left behind by other (killed) soldiers is a good explanation indeed.

Another theory is that these weapons, ammo and medikits were taken by the forces of evil as "loot" (since military bases lack other forms of treasure). Maybe they think these hi-tech gadgets are very precious tems, or an unknown form of magic. And so they hoard these items, especially in secret rooms.

Furthermore, some of these items might have been left as offerings to the Old Ones (Shubby in particular) - gifts from creatures returning from successful conquest.