Did the Japanese people consume freshwater fish during the Sengoku jidai? It seems unlikely to me that they would ignore such a resource, but parasites are more common in freshwater fish than in ocean fish, and I haven't been able to find anything definitive in the histories I've seen.
Freshwater fish such as ayu and unagi have been a part of the Japanese diet for a long time. I’ve read haiku mentioning them - I can’t remember by whom, probably Issa - and they are considered a very standard part of Japanese cuisine.
I’ve seen recipes for some other freshwater fish, such as bottom-feeders, but I live next to a river in rural Japan and I really don’t see a wide variety of freshwater fish. When I fished in a big lake once the fish were non-native.