If you give them some cover (structural leaf litter, small caves, bogwood) they will hide in / under them during the day, rather than digging into the substrate. Having said that I'm pretty convinced that they aren't your primary problem, the plants are up-rooted because they are already unhealthy.they are stirring the roots And uprooting the New plants its ending up in decay Of plants
I'd look on that as a good sign that they are happy, they aren't a fish I want to see during the daylight, I want them to be crepuscular and appear in the evenings <"The missing kuhli loaches were on the java fern hotel">.I have kept them in my planted tank with no issues apart from only ever seeing them once in a blue moon!