I'm guess that the OP has a fancy, somewhat flashy looking bike, nice parts, all shiny, clean and in good repair.
I'm also going to take a stab in the dark and assume the OP left their bike in the same place, possibly even the same rack, at the same sort of time each day, and the area has low foot traffic.

Taking these points as given, even if you used funky unique bolts the parts would still disappear. Maybe even repeatedly. Because the thief has time to scope out the bike, work out what tools are needed, and can just go out and buy them, and come back the next day to get the parts. The tools are then useful for the next person who uses the same defences.

Why would a thief go to so much trouble to steal parts of the OP's bike, well, $260+ seems like a pretty good reason. When it comes down to it if you keep putting your bike in the same sort of place, and it looks expensive, undesireable elements will start looking for ways to take the parts if they think they can get away with it.