No, Emhyr did not have 1000 Shilards. Shilard was his go-to guy to deal with the North, he was the one who negotiated the peace of Cintra, for example. Yes, one version was that Shilard wanted Geralt dead against the emperor's plans. But Shilard had no frigging idea about them!!! You can't seriously expect people to read your mind, or something. Instead of giving that stupid order to kill Shilard, Emhyr would have written Shilard directly, and order to leave Geralt alone, keep him captive if it is needed, but not kill him. Plus, it is not a good idea to execute nobles this way, without any trial and proper procedure. Aeryn Targarian, The Mad King, did not last too long when he started this shit.
The letter from Emhyr does not make any sense, at least if Emhyr is not schizophrenic. It was his goal to make Loc Muinne a second Thanedd, to get Northern mages out of the picture. Shilard's death is a failure of this plan, he had to appear on a summit for Emhyr's plan to succeed. Plus, again, as I said, Shilard was not going anywhere. What sense was it to kill him before his mission is successful??? You want to execute him? Fine, wait till he is back, provide some sort of a proper procedure, accuse him of high treason, even if it is made-up, and behead him on a Victory Square. Problem solved.