First, dumb question, but magical weapons are still considered magical if they don't have any charges, right? I'm specifically referring to being able to damage enemies immune to normal weapons.
Second, I'm looking for tips on maintaining magical weapons. The one I created only had twelve uses, so to recharge it, I would be burning through soul gems like there's no tomorrow. I was thinking of doing another with a much weaker enchantment, or doing a similar enchantment on a (lighter) backup weapon (that I would only use when needed). But, I was wondering if anyone else had any better strategies. Thanks.
Yes, a magical weapon that is depleted of charges will still kill ghosts, etc.
Regarding managing enchanted weaponry, I would avoid them until you can both repair and rechage them. Armorer skill will develop the ability to repair them. At lower levels you will encounter smaller souls, so a weaker weapon with more charges is easier to maintain at that stage. As far as going through soul gems, the artifact Azura's Star is incredibly helpful, as is including a brief soul trap effect on your weapon. http://www.uesp.net/wiki/Oblivion:Azura%27s_Star