If your son is using his own collision coverage then yes, it is proper procedure for him to be responsible for his $500 deductible, even if he was not at fault for the accident.

If his insurance company decides to go after (subrogate) with the at-fault party in the accident for the monies they pay out for your son's claim then your son may ask his insurance provider if they will be able to also get back his deductible this way. If they are then he should be reimbursed at that time.