I've never heard of "glass pipes".
Integra's have only one header, V8's have headers, 4 bangers-one header.
A header won't produce up to 12 HP by itself, it can help hit that number teamed up with a properly sized intake and a properly sized exhaust, but it won't do it on its own.
Aftermarket intake manifold's are bigger than the stock IM, allowing more air to enter the combustion chamber than a stock piece will allow. Because of the huge amount of air they allow to pass through them, they are only for moderate to extreme NA applications. Getting one for a car that only has, for example, I/H/E will kill your low end and midrange power in exchange for very small (if any) HP in the upper rpm's. You will be slower overall.
As for you origional question, heck yeah its worth it. You'll definitley fell an increase in throttle response and power, even on a car that's otherwise stock. And honestly, I'm sorry to say, putting an aftermarket muffler onto a stock exhaust system isn't doing a whole lot for you, maybe a 1HP bump here and there, maybe even 2HP up near redline, but that's being optomistic. I guess it depends on if your new muffler is a straight through or a chambered design. Most people get one just for the sound/look of it, not for a HP increase.
The stock intake has many sharp bend, resonance chambers and a filter that has very poor airflow ability. Aftermarket intakes eliminate the sharp bends, resonance chambers and use an aftermarket filter that has excellent airflow ability.