Yes, any cleaner (even soap and water) can destroy a coin's collectible value. You certainly don't want to do it to any coins that are collectable (the exception is coins that are -literally- dug out of the ground or perhaps coins that have toned so black that the date/mintmark cannot be made out at all), but when it comes to a war nickel, assuming it isn't a rare variety, cleaning it won't hurt its value since its just worth silver scrap anyways.
However, it might be very hard to get your nickel looking good because of the alloy that the Mint used which contains manganese which makes the coins turn a green-ish hue with little time and exposure to air.