The hot water boiler is separate (although in the same metal case) as the hot air heater. It is designed to have the pilot light on all the time, so that the burner can light when hot water is required. It's probably a gravity-circulating hot water heating system, so it would take hours to heat up the hot water again from cold if you were to turn it off (which you could do, using the timer, but the pilot would stay alight anyway).
If it's gas consumption you're worrying about, there's probably no need to worry. Just because you don't need hot water all day every day, it doesn't mean that much energy is being wasted if your hot water cylinder is well insulated. Any heat that does "leak out" of the hot water cylinder / heater / pilot burner is actually warming the surrounding air, so if it's indoors that isn't wasted heat as such.
Also, it's possible the pilot light itself may consume so little gas that it doesn't even register on your gas meter.... although this could be urban myth and I'm not qualified to confirm!