Normally a body shop that works with an insurance company will not pay off or discount your deductible amount. It would seem unethical. The shop may just over-inflate their estimate to cover your deductible amount with the intention of having the insurance company pay the entire amount for repairs.
If you read through your insurance policy you will see that it says that you are responsible for paying the first portion of a repair bill in the form of a deductible. If the cost of repairs comes in less than the estimate, you are still responsible for the amount of the deductible. Any savings legitimately belongs to the insurance carrier.
Repair shops should not try to hide or pay your deductible for you. This would be considered insurance fraud and penalties for insurance fraud are usually quite severe.
To find out about a specific situation and/or your state’s insurance laws regarding this topic contact your state’s insurance regulator.