For cherries, most of the videos I've seen on YouTube (of Flip Aquatics, Shrimp King etc.) seem to show bare bottom tanks with sponge filters and clumps of moss/subwassertang/so forth. Even the Caridina tanks are often bare bottom but with pots of buffering substrate put in. In short, I don't think most professional breeders have to deal with vacuuming substrate. In my own tanks, I simply don't use the python and siphon into a 5 gallon bucket on tanks with fry. After this, I let the water settle and use it to water the garden if I don't see any or fish out any I can if I do.
I've tried putting cheesecloth or a fine net over the gravel vac, but it kept too many solids from getting out of the tank and was too easy to tear. You can also crimp the hose and watch it closely, though if you have a lot of water to change might get tedious. I do find that the shrimp tend to swim/climb downward out of the gravel vac if flow is weak. And if you stick the vac end over a plant stem, they will cling onto it almost every time. Hope that is of some help, I don't think there's a perfect method!
Nothing good happens fast in an ecosystem.