No. He never did.
"Even you are partly synthetic." is:
1)An ALLUSION that Destroy will affect Shepard, not that it will kill him.
2)An acknowledgement that Shepard is PARTLY synthetic.
Catalyst never says that Shepard will be terminated, he was only warning that the wave will affect Shepard due to his synthetic implants.
EDI, on the other hand, is fully synthetic. And built from Reaper code. She's almost exactly what the Destroy wave seemed primed to aim for. Almost. Maybe that 'almost' part (since she's not literally a Reaper) could have you hope against all hopelessness that she made it intact enough. But that's far from Shepard's situation.
You're right he doesn't specifically say Shepard will be killed but he does talk about the "destroy" affecting anything using reaper tech..."destroys" beam is ONLY meant to do exactly that...DESTROY...so if he says they'll be "affected" then he is all BUT specifically stating it..and the statement makes no sense otherwise.
EDI is fully synthetic but she's NOT fully Reaper. Again it's no more likely or unlikely she could "survive" (memories/etc intact) AFTER the wave than any of the other handwaving "space-magic" we get in the trilogy. Same with the Geth. ESPECIALLY with the Geth. WHY would the beam (capital for emphasis) destroy the parts of the Geth other than what's reaper tech? it's very VERY plausible, hell even LIKELY that the Geth WOULD survive "destroy" endings by simply losing the reaper upgrade code and being back to how they were originally (pre Legion sacrifice/reaper upgrades..ie how they were in ME1 and ME2)
Now same wiht Shepard. We know at least part of his implants/cybernetics are Reaper-tech? how much we are never really told (but it's alluded to a substantial amount).....so the question, which is never answered, is...are the implants still really necessary? are they required to KEEP him alive? If I'm remembering correctly (and I may not be) In the beginning of ME2 either on one of the terminals or in one of the scenes says that they're foregoing regular tissue/organ regeneration and proceeding with implants to SPEED it up. Once shepard is fully "regenerated" those implants/cybernetics may not even be necessary. Like a cast used to help a broken bone mend. Once the bone is mended you ditch the cast. Only in this case obviously cybernetics also boosted shepards abilities...so you wouldn't just discard them.
And honestly I think the endings are supposed to be taken word-for-word..yes even staridiots ramblings. I don't think BioWare intended the endings to have near the paths people can take them in as speculation. But of course they're not really going to say so because the discussion/speculation keeps interest in ME as a whole...If they came out and specifically said "yeah guys the endings are meant at face value/as is. literally" then well interest and the topics would drop. They of course want poeple to keep talking about them and hopefully stay interested for the next part(s) in the series.
So as I said, I see no reason in high-ems destroy for it to be impossible that Shepard, EDI, and the Geth all can still survive. It's no more implausible than a lot of the "space magic" (as everyone calls it, I hate the term lol) we get anyway.