Most Enclave/BoS soldiers in their bases have guard scripts attached, that's why they can't be looted. You can change it globally in guard.fos module, see line 238 with GuardInit function:
void GuardInit(Critter& guard)
{
_CritSetMode(guard, MODE_NO_ENEMY_STACK);
_CritSetMode(guard, MODE_NO_LOOT);
_CritSetMode(guard, MODE_NO_STEAL);
_CritSetMode(guard, MODE_NO_DROP);
_CritSetMode(guard, MODE_UNLIMITED_AMMO);
_CritSetExtMode(guard, MODE_EXT_NO_WALL_CHECK);
_CritSetExtMode(guard, MODE_EXT_GUARD);
}
By removing or commenting these lines:
_CritSetMode(guard, MODE_NO_LOOT);
_CritSetMode(guard, MODE_NO_STEAL);
_CritSetMode(guard, MODE_NO_DROP);
you will make all guards drop items on death and lootable (all guards, not only BoS/Enclave).
It's not enough to just disable MODE_NO_LOOT, because anti-looting scripts are a bit paranoid and if there is any of these 3 flags set (MODE_NO_LOOT, MODE_NO_STEAL, MODE_NO_DROP), critter won't drop items on death and will delete them instead.