Throughout history why would Japanese fishermen throw back the Heikegani crabs if they caught them?

It was a matter of respect.

The pattern on the shells of these Japanese crabs ("Heikeopsis japonica") looks like a human face. They are nicknamed "samurai crab" because the face resembles an angry samurai.

Believing that these crabs are reincarnations of former warriors means that people choose not to eat them, even though they are edible.

https://en.wikipedia.org/wiki/Heikegani