Hey,
during my 100% run I've encountered a number of posts complaining about fishing and especially catching the rarer fish.
Not really sure if it actually works but so far tried it with Nishikigoi and Ghost koi and succesfully got them hooked.
Basically, it seems that the game doesn't actually unload fish that are not visible.
That means that even though I didn't see the outline of the fish I was able to catch it based on just knowing where exactly it appears normally. In ghost koi case, aim for middle between the carp and crucian and a bit more to the shallows. Tried once and it worked.
Tried this multiple times on Nishikigoi and worked almost everytime. Do try it out and let me know if it works overall or if it was a lucky coincidence!