As has been noted the chances of the destruction of Moscow are largely dependent on how the war ends. Assuming a complete Reich victory (i.e. the A-A Line is the basis for territorial transfer the result is vastly different than a much lesser, negotiated settlement.
Assuming a complete Reich victory it is almost certain that historic Moscow would be utterly destroyed and obliterated from history. The work would have been done by the civilian population as part of the planned "extermination through labor" that was to be employed to eliminate the undesirable parts of the population (the same methodology was slated to be used on Kiev, Leningrad and Warsaw). The artificial lake covering the entire city has always struck me as being somewhat overly ambitious; however, there would likely have been some sort of lake/pond that covered the region where the Kremlin once stood along with the rest of central Moscow. The hideous apartment blocks surrounding the city itself might be saved for use by the slave laborers, until they were no longer needed, then those structures would also be demolished using the same bloody-minded methods.
One of the real difficulties that one can run into regarding the Reich's plans (beyond the already noted short attention span of Hitler) is that there is a tendency to look at the plans with the expectation that they somehow, somewhere, make the slightest bit of sense. That is not something that can be expected of the Reich leadership. They operated from a shared set of delusions centered on National Socialist theory. If reality contradicted the theory then reality was wrong and needed to be ignored or worked around. The members of the Nazi leadership who were closer to reality (Speer was relatively sane, at least he could do sums and act on them while telling the Fuhrer what he wanted to hear) tended to try to find some new shiny thing to distract Hitler from whatever disaster he was creating by ignoring economics, logistics, and common sense. That frequently worked, except for cases where he wanted to see something with his own eyes. Moscow Lake would have been one of the things he would have wanted to see. If it cost a million Slavs lives to make it happen, well, in Nazi eyes,that was a feature, not a bug.
Evil bunch of bastards.