I can't find any mention of a similar problem that's related to SimpleKeys or any known incompatibilities for the application. It's far more likely that the small freezes are caused by the added stress to your system.
Judging by the fact that the application hasn't been updated in more than two years, I'm guessing that you have an older Mac model. Today's technologies, even the most basic ones such as web browsers require a lot of resources and an older device has a hard time keeping up, so any new tool that you use can bog down your system.
If the problem persists, I recommend running an alternative application such as Global Hotkey.