Man that sucks, get that hood locked down somehow, or get an alarm, and make sure you have a locking gas cap, also you could always use an allen head bolt to hold the aircleaner down, it's a little more of a pain to install the air cleaner, but it might stop or at least slow down some lowlife that want's to try it again.
I don't know what type of area you live in , but is there a place you maybe drive fast at, do burnouts at, like a certain street corner, light, or stop sign or maybe just speed down a certain street?
Is your car loud and if it is do you often rev it in the driveway while tuning it? Or do you leave home or comeback home either real early in the morning or really late at night when others are usually asleep? Maybe some loser is having a melt down because your car is waking them up everyday?
I would also talk to everyone that lives around you asking them if they saw or hear anything, and to give them your number if they ever see anyone around your car.