My brother has a 1999 EX, and I was wondering about where the MAF is...
I had a spare cone intake lying around off my Silvia, so I decided to see if he wanted it. After removing his filter box, I just slapped on the cone filter to the intake hose. Now my question is did I bypass the MAF somehow, accidentally...? What's the deal with that little U-pipe that leads to the stock air box? (and why is it so heavy?) Thanks guys!

No MAF on Honda's, they are using MAP sensor.
U-pipe to prevent hydrolocking.

ah ok, that solves it then.

out of curiosity...how the MAP work?

instead of measuring air flow (w/MAF), which is very important element in engine management, Honda is using Manifold Absolute Pressure sensor (MAP) to measure pressure in manufold but since you still need to know air flow so they made ECU to calculate air flow out of pressure.

FYI, MAP located on top of Throttle body.