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They are usually not harmful, but if you get them from the store, especially in those dry plastic tubes grown emersed, they may have traces of pesticides on them. I would thoroughly rinse *any* plant I buy, preferably soak it in water overnight.
Crypts, i hear, can release a toxic sap if trimmed inside the tank. it is recommended to remove the plant before trimming, and wait for the cut to heal before replacing into the tank.
I have anubias in my community tank, the shrimps love it as the leaves are very long lasting so host lots of food on them, I cut the leaves and stalks of the flowers from it and have not seen any problems.
The only time I have seen problems (shrimp deaths) with plants like Anubias was when I purchased them in those plastic containers where they were clearly grown emersed. It seems like there are pesticides (or whatever chemicals used while growing them) on them and unless you soak them for a day or two in a bucket with water they *will* kill your shrimp. Other than that I have not had any problems with trimming them underwater.