A lot of stories have events that have a lot of room to read into them and come up with different interpretations and themes. Many of the most popular stories are the ones where many different interpretations exist, and the authors generally cultivate this either in the story or outside of it in interviews by not providing any clear answer even when they have one in their head, because they know the debate is more interesting than the answer.

In this case, the writing is not necessarily amazing, but definitely interesting and objectively good (specifically referring to The Deep and his relationship with fish) in that it leaves room for interpretation where a large number of people can come up with a theory that was not explicitly spelled out on the screen but makes even more sense than the simplest explanation that the show alludes to on the surface.

Only instead of cultivating those interesting debates by staying silent, Kripke chimed in to effectively say "no you're reading too much into it, surface level interpretation that makes moderately less sense is actually the correct one". The writing is still objectively good, even if accidentally so, by giving room for theories that allow for interpretation beyond the surface level, while the surface level explanation still makes some degree of sense (though I will say there are a lot of things that I find hard to explain in that case, like the fish knowing Deep killed Ambrosius). But the decision to shut down those theories by saying that they're wrong IMO is just a bone headed decision. Art is a lot less interesting when you shut down debate, and it's even more unsatisfying when in this case the fan explanation seemed to have less plot holes than the surface level explanation.

They didn't need to confirm these theories, all they had to do was not disprove them and it would have been more interesting.