Hotel points are typically more flexible since they can be transferred to airlines and used for other things (including, of course, hotel stays). Typically, airline miles can not be transferred back to hotels, and booking hotels with airline miles is a poor redemption.

I'd recommend always keeping your points/miles in the most flexible places, and transferring when you have a specific need.

The same holds true if you accumulate Ultimate Rewards, Membership Rewards, etc. from credit cards... It's best to keep them flexible until you have a specific use.