So, you can read "The Doom that Came to Innsmouth" as a fun escapist deep dive in the mind of a monster, or as the symbolic description of the psyche of an individual whose acts and beliefs are... clearly presented as repellent, monstrous and totally unacceptable anyway. I really don't see where your problem lies.
I don't see a difference. For all the statements of being "alien" they still act basically human, even down to the religious extremism, misogyny, racism, and justifying their actions as not being any of those things with "facts" and "logic." (For the record, prostitutes are not the only vulnerable members of society. Whenever a serial killers targets them specifically, its always implicated in misogyny.)
The human characters in the story don't come across as sympathetic, either. If it wasn't for the "racism is totally justified against those evil fish people, honest!" part, then their actions
would come across as racist and reminiscent of Nazi experiments.
It's just repellent (which isn't a difficult response to evoke, btw) and uninteresting to me. It's just the political opposite of "The Litany of Earth." In that story the deepies are angels who can do no wrong, and here they're devils in the flesh against whom genocide really is completely justified.
This story isn't deep or meaningful, or especially respectful of Lovecraft's story. I'm sure he would find the story repellent for its sexually explicit nature, but I digress.
Continuing to regurgitate the stale trite "fish people are evil, kill them all" message is not an especially interesting premise to me.
Also, the explicit comparisons in both stories between fish people and real persecuted is pretty repugnant. Real minorities are neither angels nor demons, they're human beings. Some are innocent, but that doesn't mean all are. Some are spies or terrorists, but that doesn't mean all are.
Both stories read like blatant propaganda pieces. Aphra is a textbook SJW, Bob is a textbook mass shooter. They're not deep ones: they're human beings cosplaying as fish.
I don't know what else to tell you. Maybe it's just the result of that whole "people of different politics have different personality biases" or something.