Trying to change ballcock on hot water header tank have shut off valves under sink and in airing cupboard but still have water going into tank why?

Just guessing here but something tells me that;

You are not US;
You are talking about a small "point of use " water heater;
That you have turned off the valves between the heater and the faucet
And not the valve on the pipe bring water to the water heater.

Ballcocks are inside a toilet tank, stop cocks are small shut off valves prior to a fixture. Usually you must shut down your main incoming water line to work on most water heaters.