I'm not second-guessing my electrician, just gathering information for
later.

We agreed to install 2 ground rods, per code, and then tie a second ground
to the water supply line, also code I am told. With that they are also
going to connect a ground between the hot and cold pipes at the water
heater.

My question, what does the ground at the water supply do that the 2 ground
rods don't?
second question, as I intend on replacing all of my hot water lines with
PEX, obviously the ground at the water heater will no longer exist - am I
creating a dangerous condition or can I safely remove the metal hot water
pipes and replace with PEX - so that I no longer have any metalic hot water
pipes?