I have bee following this thread with interest and have also been investigating methods of providing additional security. I see the main problem is stopping theft, therefore, the hives need to be in a secure/obscure environment. I feel this has already been adequatly covered.
Apart from that, it is down to either making the items undesirable and/or identifiable. If the hives and frames etc were marked in such a way that it would be a lot of work to remove, then it MAY act as a bit of a deterrant, but it is the bees thay are after, so, 1 shook swarm and a bonfire later.....
I have looked at electronic tagging. This can be done very cheaply and provide a very reliable way of identifying a hive (or major component), but all I think it would do in reality is give the buyer a cosy feeling when they buy the kit. In the event of a theft, you need to be in a position of pointing a finger at someone and saying "that is mine and I can prove it" before the technology can pay for itself. Beehives are not like other desirable nickable items that the police stumble across when raiding a suspects property or a stop search. The very nature of a box full of flying stinging objects would make most of our bobbies not look, but run the other way. So I feel we would be very hard pressed to gain a great deal of support in sorting the thefts out.
I will keep looking into possibilities (tracking - out, too expensive and too much current draw to be practicle) exploding dye, open hive without key and Phut - now theres a thought, anyone seen any orange bees beeing looked after by an orange beek?