Depends on what kind you are removing, where they are located and how much exposure they have. Some can be scraped off (especially the larger ones that grow on the glass) whole, while others can be smashed in their shells or sealed in with glue or putty, the trick is to make sure they don’t survive. Snapping off the top of the tube may not kill them if they can just hide inside the lower end. Crushing and exposing them to fish predators is a great way to recycle them.
If they are digested by the tank they may show up as a small nitrate increase but you would have to kill a lot of them to measure the increase?