I'm currently re-reading Moby Dick for a book group-- this is my third reading of the novel. It definitely rewards repeated readings... something I'm finding to be true of the Iliad also, which I'm also currently re-reading. I'd say this is a characteristic of great literature.
Structurally, Moby Dick was ahead of its time. It reads almost like "experimental fiction", abandoning traditional narrative. It's something that can be frustrating at first brush, and takes a little getting used to. But I'm finding that the effort is rewarded; each time I read Moby Dick, I like it better. (Same as with James Joyce or Proust).
Structurally, Moby Dick begins as traditional first person narration. Then, as the Peqod sets sail, it shifts to an omniscient narrator. We're suddenly privy to other character's thoughts, things "Ishmael" could not possibly know. There is an interlude of theatrical prose, complete with stage directions, and then the non-fiction encyclopedia stuff, and we're off into the stratsophere....
Taken as a whole, though, Moby Dick remains a very traditional novel. The whale-ship is a microcosm, a sounding board on the nature of man, justice and laws, democratic (and other) government of men, religion, and speculations on Nature itself. It reminds me of Victor Hugo and his great "trilogy" of novels on the subjects of Religion, Nature, and the Law: The Hunchback of Notre Dame, The Toilers of the Sea, and Les Miserables, respectively.
And as for his method, what Melville does in Moby Dick is not all that much different from what Balzac did-- Balzac often got quite specific in his novels on the nitty-gritty of society and economy, matters normally outside the scope of fiction. For instance, the business of paper manufacturing in Lost Illusions.
So I think the "digressions" upon the natural history of the whale are not really digressions at all (though they sure seem that way at first...) They simply bring the arena of Nature within the compass of this rather all-encompassing novel. Something novelists, and other artists, have often done.