1) No idea, sorry I don't have a 3D TV to test.
2) Yes. I have a 2TB hard drive attached to mine right now, works 100% right out of the box (with 1.1 update)
3) You can only *directly* download apps from the Android TV version of Google Play, but you can send just about any device to the Nvidia Shield TV from play.google.com/store in your web browser, and many of them can be launched straight from the Leanback (Android TV) Launcher. Otherwise, install Sideload Launcher and they will all appear in there. You can install Chrome that way and then you can just use that as your Play Store.