What are chances of split/weakened joists from ceiling hanging hardware?
The thing is you are screwing against the grain - which is exactly why home construction is done the way it is, almost making it impossible to have to screw into framing with the grain.  

Meaning you could easily put screws a good 40-50% of the dimensional thickness of the lumber with no repercussions.  You could put in those hooks every foot on every rafter and they would have no impact at all.  However... With hooks and screws usually comes weight.  Bikes are no worry at all but if you start hanging large shelves in the middle of a 16 foot span in a garage, you should worry about sag.  That is a different question though.