If you go the extension cord route, I would get the best gague cord you can afford and the longest. one long cord would be better then two shorter ones.
If you have to use two shorter cords I would wrap the junctions with electric tape.
There is always a chance of things going wrong with electric and water. I have heard of horses being electrocuted, and when I was younger we had the watertrough shock all of our horses, it was 4 months before they would walk next to the trough and 6 months before they drank from it again.
I do not know if you can put a stock tank heater in a rubber trough or even a hard rubbermaid trough, mine are 100 gal galvanized, and some horses play with the heaters at first.
What i did was, first time I turned on the floating tank heater, I did it during the day when I was home, and for about 3 weeks I unplugged it every night and plugged in every morning untill I was sure it would work.
I cannot stress how important it is that the heater is plugged into a GFI, If anything goes wrong it will, in theory, trip and cut off all electricity to the heater.