This is a big question in Jewish law. Classically Jewish law permits parasites in fish that grow in the flesh of the fish (which is what I assume you're talking about with the microscopic shellfish), but not ones living on the fish's skin or in its digestive system. The issue is that the parasites do ultimately get there by being eaten by the fish (which probably was unknown to Rabbis in generations past), so there are periodic debates on the permissibility of fish known to have parasites.

The consensus is also that Jewish law doesn't care about anything microscopic, no matter the source. However, availability of the microscope meant that Jews became aware of various sorts of insects that might be visible to the naked eye, but only if you know what you're looking for, and aren't identifiable as insets to the naked eye. This causes considerable discussion of the extent to which vegetables, especially leafy ones with nooks and crannies for bugs to hide, need elaborate process of washing and checking. So even though the explicit Jewish law remained that microscopic creatures present no kashrut concerns, the availability of the microscope did alter the ways Rabbis and lay people were concerned about very small insets in food.

This is a nice piece on exactly this subject: https://hakirah.org/Vol22Adams.pdf