How is a 29"er different from any other 700c hybrid? Is it the amount of tyre clearance?
If you are buying a bike for commuting you may as well get one that works well without hack solutions such a P clips.
Look for an ISO disc mount on the chainstay not the seatstay. This will free up the standard rack eyelet for a standard rack. Some Scott and Trek bikes have this.
Make sure the bike has proper rack/fender eyelets.
Do you need a suspension fork? It is hard to integrate a good fender with most sus forks.