Yes. Even though the hit-and-run accident was not your fault, the collision deductible would be due as part of the claims process.
Whether you are at-fault or not for an accident, when you make a claim under either your collision or comprehensive coverages the deductible amount you chose at the inception of your policy is due.
Hopefully, you made a police report about the hit-and-run incident. If law enforcement is able to find the driver that did the damages to your vehicle, then you could go after that individual for the deductible amount you have to pay out of your own pocket.
Your car insurance company would also go after the responsible party, if found, for the monies they pay out for your collision claim.
The only way that your deductible would not be due is if your auto insurance provider waives it for you, but that is not normally done in the case of hit-and-run accident claims.
Contact your agent or your company's claim department to start your claim for the damages your vehicle received from the hit and run accident.
If your agent is not able to explain what to do in this situation, or fulfill your car insurance needs, contact a CarInsurance.com agent. Our agents can explain not only insurance terms and claim procedures but also tell you how they can get you low cost car insurance.