kungfujoe, this is a know bug, that has its own (many threads).
I have another idea about the initial scarcity of weapons:
UN directives say "one primary weapon and one sidarm is enough for every soldier, we don't want to see any weapon leak or any half-official additional hiring of soldiers". Moreover their procedures regarding miliary installations, and Phalanx bases in particular, require basic military training for all employees and at least a sidearm for each employee. This is so strict that no employee is allowed to be weaponless, so if you want to unequip a weapon from an employee you have to assign him another weapon at the same time (this requires a slight UI change to allow one-drag equipment swap, which is currently possible only for armor).
So, actually, there is plenty of weapons in each base, assigned to the employees the player is commanding manually and to all auxiliary personel that is known only from the additional fixed montly upkeep of the base. But still, there are no spare weapons until the commander manages to wrestle some, riding on the fame of his succesful missions and arguing that weapons need replacement after missions (but he does not want to hand over the old weapons, which makes this argument not so successful, anyway).
This idea goes well with the idea to be able to take some non-soldiers on missions (see the wiki), as well as with the idea that in the absence of soldiers, a militia is formed from other employees to defend the base (but, e.g., only if you have Team Room in your base). I guess I'll make a patch that autoequips every employee on creation, so that this works well without player work overhead.
