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Short of drilling holes, I guess a decent chain and pad lock is going to be the most secure option. Hopefully your boat has something sturdy to fasten the chain to though. Not much use if it's fastened to something which only requires a screwdriver to remove.
I'm a bit wary of the Transom as it is (future project) so don't really have anything to attach it to. The above seems like a good idea. Another suggestion is to change the bolts for ones with security bolts(like you get on Alloy wheels)