Would like to point out that in my experience most men who use that expression (at least that I have run into or in popular culture) say "trophy wife" when they mean someone who is attractive and that that is their main redeeming value.

So for example one wouldn't have called Hillary Clinton a "trophy wife" because although she is quite accomplished she is not really of the grade of looks that would be "trophy" (in the common usage).

Ok so now I go and seek the definition on the internet to see what it says. And it says this:

"a young, attractive wife regarded as a status symbol for an older man."

That said of course you are right that "trophy wife" does not mean "not intelligent" but that is most likely the assumption that the majority of people are making.