Will using a Chimney Balloon to insulate my fireplace block the ventilation of my water heater and furnace?
You should check whether there's a single flue for all three utilities, or multiple flues. Generally (and I think this is code, at least in the USA) fireplaces shouldn't share their flues with anything else, including other fireplaces. My (1960 Massachusetts) house has two fireplaces, a furnace and a gas hot water heater; it has one flue for each fireplace and a third shared flue for the heat and hot water. If they're separate, then you don't have a problem.

If indeed a single flue services all three, then you'd need to find out where the furnace and water heater's exhaust join the flue. More importantly, I'd be worried about safety even without the chimney balloon; it would be easy for carbon monoxide from the water heater and furnace to come down into the fireplace and into your living room.