question about factory intake system

I understand that the plastic blocks attached to the fresh air tubing prior to the cleaner are called mufflers but do they serve any other purpose? my Honda fit has the as well but I sure dont understand why. also if I chose to remove the rear most muffler and run a section of pipe there to the tail end would it be an emissions issue? i am not removing the cat or the resonator just the muffler.

While technically illegal to alter your exhaust in any way, the fact that aftermarket exhausts are totally unregulated points to the fact that they really don't care. Pretty much anything after the catalyst is fair game to do what you want. As long as its not so loud that they can cite you for a noise violation, its mostly unregulated.

As far as the intake tubing, it depends. Most factory intakes are adequate, and altering them either improves them slightly or not at all. Most of the baffles and other things inside them are to keep intake air quiet so you don't get that "roar" when you mash the pedal.