Will I be charged more for prepaying by credit card when booking a hotel room?

No more money will be charged. When checking in, swiping your credit card is pre-authorized, which means that part of the money in your credit card is frozen. When checking out, swiping your card is done within pre-authorization, which means that The money you spent this time will be deducted from the pre-authorization, and the remaining money in the pre-authorization will be unfrozen and returned to your credit card, so there will be no overcharge