Good question @Luke -- I should have included that! I don't use the web app that requires Emby Connect (as I've not set that up yet), but the web app that is built into the server does not show these Extras any more either.
I should mention that I don't remember for certain whether back around April 1 I was checking within the server web app, Emby Theater, or both. But it would have been at least one (and likely both) of those as those are the only two Emby apps I use (and I typically check both, but especially Emby Theater, when I'm trying out something new).
It has also occurred to me that this might actually be a Server issue, ie, it might be that the Server is no longer "registering" these items or something. So I just did a test of adding an Extras folder (containing only Media Stubs, in the form of "name.disc") to a Movie folder (in this case, the movie is also a Media Stub), performed a Library Scan, and found that there's no mention of the Movie ("Dawn of the Planet of the Apes (2014).hddvd.disc") or the Extras ("Special Features (Online).disc" and "Vudu.disc").
I'll send you the Log via PM in a moment.