The bottom won't look like Yosemite but all the studies have taken this into account. Because the reservoir is so high in the mountains, and because of the local conditions, they have measured very low silt buildup at the bottom. So it is expected that it will be bare for a few years, and within maybe 20 years it will be filled with new growth and start to regain some of its splendor.
I am no liberal on these matters but many have said that Hetch Hetchy was more beautiful than Yosemite before it was dammed. If the water can be replaced by water from the California Aqueduct then I think they should do it.
It would be poetic justice if they found an "endangered" lake dweller, that was "dependent" upon the current conditions, thus hoisting the driving-force enviroes behind this on their own petard..