While I do think it is a good point, Obisgirl, that Emma can (sometimes) be intuitive and smart*, she doesn’t have any reason to connect those dots as opposed to thinking that Hook broke a deal with Gold, and Milah paid the price.
The way Hook talked about what happened with Milah, there’s no hint that Gold killed Milah for anything but to hurt Hook, not Milah, the same reason Hook is going after Belle.
Plus there’s Neal’s age, being relatively around the same as Hooks to Emma’s eyes. While big age gaps happen (especially on this show, due to frozen, looping time!) I’m not sure Emma would immediately think of Hook going for a lady old enough to be his mother biologically. Turns out, Milah probably was older than Hook (hard to say how much, timelines and ages…save us!) but Emma is still wrapping her head around these people living for 100’s of years, or at least, having been born 100’s of years ago.
*About Emma’s smarts, I think all the characters suffer from occasional bouts of diminished intellectual capacity for plot necessity or humor, particularly David “but I’m his Grandpa” Charming.
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass