My stem plants (e.g. bacopa) have roots growing from their nodes (not buried in substrate but exposed in water). Should I cut them or do I leave them as is, to permit them to absorbe more nutrients from the water?
You can cut them if you don't like them. I doubt it will change uptake that much though, cutting roots usually promotes new root growth, so you may actually be strengthening the lower parts of the roots by doing so.