The fact that you specifically went to a "pre-approval" site, which identifies it as a loan application site, makes it almost inevitable that your credit will be checked. I'll bet that if you read through the fine print of the online application, it will indicate that you are giving them permission to pull your credit.
Dealers often try to group the purchase price and the loan application together in the the negotiations. If they run your credit and find that you have a low credit score, they might agree to offer you a lower price because they know they're going to make a killing on interest charges.
