Update October 15th: Youtube has returned to using the Flash-based video player which supports 3D viewing.
Back in June, Youtube announced they were working on many new features: YouTube Creator Blog: Look ahead: creator features coming to YouTube.
One of these is support for 48 and 60 frame per second video, as illustrated in these demonstration 720/60p videos on Youtube. Supposedly several channels on Youtube have had 60p capability enabled for testing.
My guess is Youtube has placed a higher priority on their published feature list and likely other features not yet announced (including additional capabilities to completed features such as Creator Studio)- and not on their unannounced shutting down the 3D video player. There are many capabilities yet to come such as improved integration with other Google Services (they’ve just added a way to link in Google Photos, for example).
At some point, 3D will come back. But Google did not support their own Youtube 3D player in their own Google Chrome browser which sends a strong message that 3D has not been a priority at Youtube for quite some time.