Only question about that theory is... how would 47 make money? He's gone rogue from the ICA now and is on a "personal" journey. He's no longer doing anonymous contracts for cash, he's hunting and killing the people involved in the Victoria conspiracy. Maybe the money system can work like this: 47 has a sympathizer within the ICA who feeds him weapons and equipment. The more of a mess 47 causes in missions, the harder it is for the supplier to cover his illegal dealings with 47 since he's showing up more on ICA radar. More points=more guns available.
I like that idea, but don't think that's what we'll see in Absolution - I think they're really putting 47 on his own in this one. It may be that, while most of the levels are chasing down and taking out the conspirators, every 3rd mission or so is done for a random client that 47 has gotten in touch with personally (instead of through the Agency). Not dissimilar to how he takes out the King of Chinatown for Birdy in return for certain information. Idea would be that, in order to continue funding his search for the truth, every once in a while he has to take on a paid contract. I don't know how likely this theory is to be true, I'm certainly not hanging my hat on it, but it would be nice if earning money and spending it on things like weapons was still a part of the game.
If it's NOT money in this one, then I would hope that weapon collection/upgrading would be done just by finding the weapons and exiting the level with them in your inventory, H2:SA style (I think that, as others have mentioned, the car we've seen 47 driving a few times will serve as a mobile "safe house" and weapons stored in the trunk will be the basis for pre-mission weapon selection - see Saints trailer). Either money or the car-trunk inventory would make sense within the game world... "points" from your mission performance allowing you to obtain or upgrade weapons would break immersion significantly and be a shame imo, so I really hope that's not how it's done. Again, I'm fine with these points allowing you to upgrade "techniques" like point shooting and blending-in, that has more of a xp --> character progression feel to it, and works within the game world in a way that "oh wow I was really stealthy on that last assassination, so obviously my 'baller has magically procured a red dot sight on it" just doesn't.
Nov 20, 2012: Agent 47 suddenly discovers a hole in his pocket. A black hole.
R.I.P. Physics (dawn of time - Nov 20, 2012)