It's possible to cut the headers, lose the crossover, fit shorties, and fabricate a "baffle-sleeve" that's a slip fit into the cheapo shorties...this sleeve is really important, as it has a concave reflector closed at the engine valve end, and has regularly disposed holes in the skin > (holes about 5/16 and deburred) total cross section area > than the inlet) and a snuff or not at the street end, which has to be a slash cut so you can fit the snuffer. Of course after that, wrap the pipes and seal with silicone RTV spray to keep the Reynolds Number sweet. I posted the exhaust length site recently... it's worth reading, a lot >
http://www.nightrider.com/biketech/calc_exhaustlength.htm Building that stuff took me several days, first of study, then of thought, and thereafter a lot of work. The kid was coming to go riding... (he's 46).
The reason the stock header pipes are double wall is to keep the gas stream as hot as possible. This is important and vastly lowers the friction once things are busy making some good power. The convex reflector is very important - there is a lot going on in the pipes, which are "traveling wave tubes" with mass flow and also acoustical energy interacting. Look >
https://en.wikipedia.org/wiki/Reynolds_number
I'd leave it alone, and not drill anything. Save up the bread and buy a complete system. But your "need for noise" = need to be seen...so a few holes as Brother James has shown, neh...why not?
The reason I know it is possible to design-build with the cheapo JC Whitney shorties is that I had/have an XS that the previous fella had drilled as you speculated, drilled the mufflers to make it louder... As to carbs.> flatside Mikunis. They're bitchy as el. The cheapo shorties? They were in the shop junk pile, the guts fell out, all rusted away...but they look nice now. And they're kinna loud with the snuffers open.
I'd stay with the stock tooters. Stock exhaust. Let the scooter tell you what it wants...ride her and listen. Make dialogue. Couple thousand miles and y'all will know all about what the old gal wants.
Best o luck. What you learn to do is better than money - nobody can take skills and knowledge away.
NB> The nightrider site is less than it used to be...see this>
http://victorylibrary.com/brit/mega-c.htm