I sanitize the hot water heater along with the rest of the system.
Just be sure to drain the water heater and flush it out when you flush out the rest of the system. I "remembered" to dump and flush the water heater when I took a shower that first camping trip of the season. I smelled chlorine and came out of the shower smelling like I had been in a public swimming pool. Not a big deal, but yeah...
Here is a recent thread.
Sanitize in bypass or not?
2006 Sunseeker 3100SS/LTD
2008 Smart Passion Cabriolet TOAD
1986 Honda Helix (Original owner)