Several options. I have the exact same set up.
1. Buy the expensive Thule lock for peace of mind, has a long body for attaching the lock mechanism with the hex head accessible away from the tight confines. This is the route I took.
2. By an allen-head or torx metric bolt (thinner 12 point socket). Per another member's suggestion, use a cordless drill with the hex bit driver for easy/fast off and on. I have two allen head "spares" just in case.
FYI, my threads in the Thule were dinged and I can only thread the bolts on the left side. I will need to get a metric tap and clean out the right side if I want to use it. That being said, when the left side has been torqued down, I have found some loosening of the bolt after long trips. I may consider cutting each allen head thread body shorter and threading from each side to decrease the degrees of freedom of motion.
As far as security, I chain my bikes together and weave through the carrier, though that would probably not deter a determined thief.