Those are called aerial roots, they are a common feature of most fast growing stem plants. Its one of the ways they take in nutrients from the water column and also how they can anchor themselves to rocks or soil on banks of ponds/lakes (they are marginal plants which grow both submersed and emersed in nature).
From my own experience, what i've noticed is aerial roots usually pop out on older stems (it doesn't seem to matter if the soil is high nutrition or not, aerial roots still grow out eventually).
If you find the aerial roots unsightly, just do more regular uprooting and discarding of the old bottoms, and replanting the newer tops... alternatively, just trim off any aerial roots you see as part of regular plant maintenance.
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