Like I said, if in fact Simon's body was never found then that should have set of all kinds of alarms in the White Council. Them simply assuming that he was dead and that the body had been destroyed or removed is the least likely of all possibilities.
First, it's just never wise to assume that a member of the Senior Council is dead until you see the body. Harry himself has cheated death, and he doesn't have nearly the power, subtlety, or experience of someone like Simon Petrovich.
But even more important, the WC could not afford to make that assumption. If they were wrong, then the logical assumption was that Simon had been taken alive by the Red Court and that a member of the Senior Council was in danger of being turned into a vampire. If that happened then the Reds would gain an enormously powerful new member and a fatal load of the WC's most secret information. The had to either make sure that Simon was dead or find him (and either rescue him or kill him).
I grant that the case for Simon = Cowl is a strong one, but if it turns out to be true then the story needs to explain how Simon convinced the WC he was dead, and "the body was missing" is not going to do that.