There are good reasons for keeping them in pots, for example, if you have a lot of fish which burrow in the substrate and uproot everything. If there is no real reason, it is better to remove the plants from the pots, cutting the pot away if necessary to prevent damaging the roots.
Cut of any obvious dead root material, use sharp tools, you don't want to encourage rot.
Frequently "a" plant in a pot, not just stem plants, will be several, and you can spread them about a bit.