All substrate should be vacuumed at some point, preferably during PWC's to remove excess food, waste which will just help keep your water cleaner. However, many members ... myself included ... do not vacuum where the plants are. The ammo that produce by the excess food and waste can be used by the plants.
Most substrates are ok for plants ... the question is how high end do you want to go on substrate. Some plants require more nutrients thus maybe a mineralized soil is the way to go. However, I find Pool Filter Sand works great. It's small enough for roots to anchor, and just large enough not to cloud if disturb. In the end it's really up to what look you like most.