Yes, if use booking.com (or any other third party) and there is any problem with the reservation and the hotel doesn't have a room for you, they will point you back to booking.com and say there's nothing they can do (which may be true).
I always book direct with the hotel. Saving $5 on a room is not worth showing up at 11pm to find out they don't have your reservation.
I once used booking.com to book a block of several rooms for a wedding. Paid and confirmed. When we arrived, the hotel had no record of our reservations! The explanation was that their sync with booking.com was prone to failure and hadn't been updating for several weeks and they hadn't noticed. Luckily, they still had enough rooms available for us, but I will never use a 3rd party site again and I will always call ahead to confirm the reservation is still on the books.
I always book direct with the hotel. Saving $5 on a room is not worth showing up at 11pm to find out they don't have your reservation.