I cant say if modding a stock VS650 exhaust is better or worse - thats up to you.
I can tell you, years ago I owned over a dozen different air cooled VWs (beetles, campers....)
the stock exhaust tended to be expensive and only lasted a few years with salty roads. I use to buy headers for my VWs.
You could get a set for half the price of stock exhaust, but it was somewhat loud, like a glass pack (but it was steel).
For about twice the price you could get headers with a quiet muffler.
I have to say I liked the headers with the quiet muffler better, esp on long road trips. Dont know how you intend to ride your bike, but for me the constant drone of loud exhaust is not a positive quality.
How loud is too loud? One of the quietest cars I have owned was a new 2000 saturn SL (base model) 5 speed. On the highway at 70mph the only thing you could hear was the tire noise and the radio antenna kinda whistling in the wind. I actually took it off once for a few weeks, and I loved my silent car.
But thats just me.
Ride your bike for a while. Once you drill out the stock mufflers you cannot un-drill them.