The first thought I had was it would be a great gesture if you paid his deductible. Then I thought better of it. That would open a door that you may not want opened. His claim is that the site was "unsecured". What does that mean and what is his expectation for security for his vehicle? Had he been to this site and other equally "unsecured" sites before knowing they were "unsecured"? What responsibility do you hold for the client's site security? If the site is a company site was the company negligent in some manner that contributed to the theft or was it a random act? Has such a theft occurred before and if not how will you handle similar thefts? Would you accept responsibility if the theft was personal property from the vehicle? What if the theft occurred while traveling from one client site to another client site? Would he expect your company to pay for "security" for his vehicle while traveling? Was he negligent by leaving his car unlocked or leaving the keys in it?
I am sure you pay him some type of mileage or stipend for using his private vehicle but that does not convert his vehicle into company property. I do not know how many employees you have that must use their private vehicle while working but think of the precedent you will set. I would really think about that. Might be a good idea to consult your company's attorney before you approved or disapproved the request.
Just my thoughts.