I don't think there is any constant time it adds to a VI's execution. However, it does make sense that it would take longer. Custom probes are really just subVIs that run when execution reaches them. Once execution reaches them, the probe has to fully execute before your application moves to the next subVI. As a test, I created a custom probe which just had a wait function and waited for 5000 ms. It added 5 seconds to the overall execution time of my VI. So, any code you put in a custom probe, whether it be simple comparisons (neglible change in performance) or even full data acquisition (more change in execution time), a custom probe will add to the overall time of your application.
J.R. Allen