It should toggle between reaper trying to set the device's sample rate to match the project and the opposite, which would be to respect the sound card's current sample rate and just resample the project to the sound card's rate on the fly during playback.
If I'm correct there, then the latter would be more likely to cause pops and clicks because resampling on the fly incurs more CPU overhead. Usually the little "i" on media items will turn blue if it is resampling on the fly FYI and will tell you so if you hover the mouse cursor over it. You generally don't want it blue/resampling if you don't have a specific need (such as tracks with different sample rates).
However, if you are using ReWire/Reason, I suppose there could be a conflict that occurs between the sample rate Reason is using and Reaper, and unchecking it solves the conflict, but that's a bit of guess - IOW, same problem, different neighborhood.