If you run 3 of the 4 bolts, there might be a little vibration from it not being balanced, but nothing serious. It is ok to run the three bolts for now. You should really get another bolt so you can run all 4. The bolts screw into the water pump, not the pully. It just goes tough it. Just go to the local hardware store and buy the exact same bolt with a lock washer. Since bolts are so cheap, I would just go buy 4 new ones, just so you don't have to worry about them breaking again any time soon...
