You can cut roots, but it will cause the plants some shock. In Bonsai techniques they trim or cut the root mass and they do it for mother plants. I will post an article in the indoor growing that talks a little about it. If you cut the roots what kind of system do you want to put them in? Soil IMO is what I would use and many folks who even grow hydro keep their mothers in soil because it is lower maintenance.
If you go and transfer them into soil I would use some rooting powder, I am not talking about cloning powder, but a good transplant powder. I use Macorsi I am not sure of the spelling, pronounced Mu-cor-zy. I sprinkle this on the roots of the plant I am transplanting and in the hole of the area that I am potting in. When I transplant I get no visible shock. Hope that this helps some.
Adieu