Given the nanotechnological nature of the nanosuit, and the amount of biological integration with the pilot, it is likely that waste disposal is handled by the nanomachines within the pilot's body. (e.g. they simply break down the waste before it has to be ejected by conventional means)
As for the attachments, the same goes for extra magazines, grenades and other inventory items that would otherwise be too bulky to carry in the real world. They always just manage to materialize out of thin air when you need them. I seriously doubt the developers gave it that much thought when they designed the game. I mean if video games were 100% realistic, they wouldn't be any fun, would they?
[Edited by oljo0704, 3/26/2011 10:43:04 PM]
[Edited by oljo0704, 3/26/2011 10:45:00 PM]
If this was true, he wouldn't need to carry ammo. The breakdown of waste makes a certain sort sense, because some of that can be re-used by the body.
Ammo, however, does not; you cannot create anything out of thin air, which is essentially what you're saying the nanobots would do.
However, if Alcatraz had a location to store each of these items, the weight wouldn't be an issue... face it, he's ina suit which basically makes him supar man.