They are not familiar with the Sha from the inception. It blindsided them, doesn't mean they aren't quick to learn. They discover the sha energies through your efforts, when you bring back fear-tainted Amber.
Yes there is a connection, but it hasn't been explained. It doesn't mean the Sha are "Y'shaaj's essence" or ghost or whatever. The Sha could just as easily be Yshaaj's version of faceless ones. To say, with certainty that the sha are "exactly this" requires proof of such a claim and there isnt any just yet. All we have is the Pandaren account, which says they came out of Shaohao and were defeated and trapped by him, and the Shado-pan saw to containing their influence around Pandaria when the empire ceased to be.
---------- Post added 2012-11-10 at 12:39 AM ----------
Even the whale sharks out at the fatigue zone don't one hit a player, well not a level 90 anyways