Quoted:
I'm not at all familiar with the C50. Is it carbed or fuel injected?
Sounds too lean, it either needs to have the carb(s) rejetted or the ecm remapped to provide a richer mixture.
As stated above, less restrictive exhaust will flow more air, so you need to throw more fuel at it to balance it out.
The C50 is fuel injected. It's immediate predecessor, the Volusia, was exactly the same, just carbureted.
I'm in agreeance with the above - popping is a sure sign of a lean condition. All bikes sold these days are jetted/programmed to be very lean, as emissions regulations have gotten a whole lot tighter over the past 10 years. It's actually very normal, but some people don't dig it.
Time to find an ECU tuner of some sort and richen up the low-end/idle fueling a little bit. That would probably solve the popping-on-deceleration issue.