People who read the word "chant(e)y" before they ever heard it spoken will naturally pronounce it like "chant."

Whall (who went to sea in the 1850s), Hugill, Doerflinger, and all other writers on the subject go out of their way to say that, in their experience, "shanty" was the only pronunciation used by sailors.

Which, of course, is the biggest strike against a derivation from "chant."