The idea of using tamper-proof hardware is a good one, but unfortunately, it’s pretty normal for there to be no need to grip the bolt/screw head when removing the nut, and even if there is, such as due to the use of nylon locking nuts, lightly gripping the leftover end of the bolt with a pliers will defeat this system in this case. On that same idea, though, you could simply squash the threads on the end of any bolt that extends beyond the nut (a Vice-Grips will do this quite easily), or even bend the tag end of the bolt sharply enough to prevent removal of the nut. When the day comes that you want to disassemble that part, you’ll need to get a little creative (a short piece of hacksaw blade gripped with a Vice-Grips will do the trick), and with any luck, more creative than the average opportunistic thief is prepared to be. Of course, a thief could cut the thwart with a saw, but probably isn’t highly likely because now he needs to fix the damage before selling or using the boat. I can think of a way to add a non-saw-able insert to thwarts, which would be extra work and expense for you, and probably an extra half-pound of weight.
If you really want to get elaborate, install a “Tugeye” at one or both ends, and figure out a way to make that the attachment point for your locking system (Google “Tugeyes” to see what this is about, and to also find links to do-it-yourself substitutes for the brand-name version).