I can't say that I am convinced that miscenegation is the central theme of Shadow over Innsmouth. It seems to fit the recurring theme of personal body horror that you see in stories like Facts Concerning the Late Arthur Jermyn and His Family, The Rats in the Walls and Pickman's Model, which I have the impression reflect on Lovecraft's feelings towards his parents, who both died in mental institutions, and how his mother is reported to have call him grotesque or malformed on occasion (possibly due to her fragile mental state). For example, I've never heard that Lovecraft was anxious that he might secretly have, say, African or Jewish ancestry. I can see how the story can be interpreted that way, or both ways, but when holding it up to the aforementioned stories, two of which also feature the destruction of the people involved through suicide or murder of the people involved, but otherwise cannot be said to have any bearing on miscenegation in the US, I think this might be a case where ancient evil fish people are by and by ancient evil fish people, and not a stand in for migrants or the descendants of former slaves.