Actually, when you are growing rooted plants, you do not dig into the gravel at all while Pythoning. You just pas the intake tube lightly over the surface of the gravel to get up any surface debris. Mulm in the gravel is providing plant nutrients.
If you are removing a large clump of Crypts after they have been growing and multiplying in place a year or so, then whle they are out you can vacuum out part of the mulm if it seems excessive, but not like in a FO tank.