I can state categorically that they are BOTH very poor insulators, so a difference would be near immaterial.  By far the highest heat loss of an RV is through the windows.  Even if glass was worse, I'd consider the clear view, lack of distracting scratching, and glass being 100% unaffected by UV damage to be insurmountable. 

I was thinking the same thing about the degradation over time. Any opinions or experience with the difference in insulation properties of glass vs poly-carbonate?

Has anyone installed a Propex hs2000 heater in their rig?

I do use my Sunrader “Louise”, as a ski chalet actually. My only heat source at this point has been a Dickinson Marine P9000 which I installed where the radiant heater used to be by the entry door on the wall behind the passenger seat. I removed the electricity sucking original furnace years ago. On a cold winters night I have been doing these three things to warm up Louise: (1) turn on the Dickenson P9000, (2) boil a liter of water on the stove top, (3) run the 22re and vehicle heater on high fan speed. Once the water boils I pour it into a Nalgene bottle and throw that into my well blanketed sleeping chamber. In the time it takes to boil the water with all three of those heat sources going - the cabin is comfy so I turn off the engine and set the p9000 to low to maintain the temperature. All this while temps outside are in the high to mid 20s (Cascades/Siskiyous/Shasta). 

I removed the water heater this week as I have not used it ever. Speaking of that I also have not used the interior plumbing. The system has a leak in the small bathroom sink region (could be solved by replacing the faucet in there). The plumbing is the original stuff and I don’t really trust it. 

My thought is this: install a Propex hs2000 with a “Y” junction, giving me the option to direct the hot air to one of two ducts. One duct would be vent out beneath the stove - the other would go through the wall and into the shower stall in the rear bath which I plan to convert to a drying closet for wet ski gear and boot liners.