I'll have to go back and re-read the CM tech manual to see what it says, but I can't remember if the EEV's were dedicated just to cryotube evacuation, or if it would be used as a normal escape pod for the Marine crew of the ship. If it's a cryo-only vehicle it would make sense(What use are weapons when an enemy would find you in cryo), but if "live" Marines could use it, it would be kind of wierd an escape vehicle for a warship wouldn't have some sort of emergency armament for evacs in hostile territory, even if it is just a survival kit with 2 stowed away Pulse Rifles. (Unless they expected to bring thier own gear)
Either that or there were weapons on board, and they got lost during the crashdown, or nobody thought to look for 'em (or couldn't access them).