Do I need to turn off my Water Heater when changing my hot and cold bathroom sink flexible water pipes?
The water heater should have an vacuum relief valve, so no siphoning should happen. The water heater is designed to withstand a loss of pressure on the cold side without any problem, no matter if the hot tap is open or not. 

Consider this: if you close the main shut-off, this has exactly the same effect if the water was turned upstream from you, on the street, or if the water main burst somewhere, etc. So this poses no hazard to you or your water heater, as these things happen from time to time, and your water heater is designed to handle them.

Just close your main water shut-off, open the taps you are changing water pipes for, both cold and hot, and let the water drain. Hopefully your main water shut-off is operational, and withing a couple of minutes, water stops flowing, then you may proceed. But wait till the water is completely stopped: any trickle may indicate that your main shut-off does not close properly.