In the game's files are two unused texts regarding the Hylian Loach. This may suggest that said fish would've been found in both a bottle and without one.

The first text states:
"It's a Hylian Loach in a bottle!
An illusory fish that
few have caught...

And it came in a bottle!
What a find!"

Another one states:

"You got the Hylian Loach!
An illusory fish that
few have caught..."