Yes, economists really do study all sorts of things. Tyler Cowen points to a study of the effects of gender transition in the workplace:
We find that while transgender people have the same human capital after their transitions, their workplace experiences often change radically. We estimate that average earnings for female-to-male transgender workers increase slightly following their gender transitions, while average earnings for male-to-female transgender workers fall by nearly 1/3.
Sadly the paper that Cowen references isn’t available to non-academics except by subscribing to the journal in which it is printed, so some of the assumptions in the study are not at all clear. I would like to know, for example, whether the people studied were known to be transgendered at their workplace, as that can make a huge difference to how they are treated.
But basically this comes back to what I was talking about in the Gender Balance Question: “the idea that women should naturally aspire to be more like men, but that no man in his right mind would want to be like a woman.”
And if you really want to know how badly women are treated in the workspace, ask a transgender woman who has transitioned mid-career. Someone who has grown up female in a society where women are routinely discriminated against can become used to the effect and stop noticing it, but someone who suddenly discovers that their opinions and skills have dropped precipitously in worth simply because they have become female sees the issue very clearly indeed.