I have that same heater in one of my tanks. I had one for about 2 months that clicked/popped every time it turned on to heat the tank, and then it starting making crazy loud popping/knocking noises that seriously sounded like a glass tank breaking from a pressure crack. At this time, the heater stopped producing heat.
I replaced it (thank you customer satisfaction guaranteed!) and the replacement makes a tiny, tiny 'click' whenever the heat kicks on, and it has been running with no problems.
It definitely is my biggest complaint by far about the heater, but unless it stops working, I don't think the pops are an issue. My betta didn't seem to mind the noise/vibration at all, and he liked to hang out right next to the heater.