Same issue here only a different bike. I own a smooth riding 09 Sporty 1200L and just got 14 Dyna FXDC with V&H slip ons. It vibrate badly and not comfortable above 60 mph. You might be right and it has something to do with the pipes.
The sweet spot on mine is around 65-70 mph, it smooths out nicely. As a matter of fact, my Sportster is smoother at speed than than the Honda VLX I traded for it. The VLX would buzz my hands until they would go numb at 65-70 mph, and the handlebars on it were rubber mounted.