Hot glue is best for the probes and you want the probe on the hottest spot in the enclosure that is accessible to the snake. So you want the probe on top of the glass, under the substrate.
The problem with Velcro is that it does have sticky adhesive that is used to stick to the back wall of the enclosure and on the thermometers. There should be no sticky adhesives in the enclosure. Someday it could start unpeeling and stick to your snake..