Each thermostat should have a "max" wattage - Going over that may over load it and cause it to not function properly or it could be a fire hazard. The one I have is rated for 1000 watts, the CHE I use is a 100 watt. I think it would be difficult to over load one, but unless you go over that rating it should not matter.
As for wattage of the bulb the higher wattage will put out more heat. A 100 watt bulb will heat a larger area better than a 50 watt bulb