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There's no reason he'd know who Santa and June are because their names are kept secret and they're adults now, and even a non-prospagnosiac, I think, might have trouble recognising them perfectly?
So the only part left is that he never kills Clover. Snake is likelier to recognise Ace's voice and is pretty smart, so he presents a more immediate threat to take out.
But he would presumably let Clover in on it if they were ever alone together. That never happens! The only time Clover gets with Snake after they meet Ace is when they're with Ace himself. Either Ace and suspicious amnesiac Seven go with them into Door 5 or Junpei goes in instead of Clover and Ace. So they never have a chance to exchange that information. And Clover isn't suspicious of Ace outwardly, so she seemingly hasn't cottoned on herself. After all, she was a kid when she was in the first games, and most importantly: we don't know if Clover ever met him, but we know that Snake did.
Snake was on the Gigantic, and he was left behind with Akane/Santa/Nona/Seven, who got caught. Clover was in Building Q, however, and might never have had to run into Ace. Presumably Snake told Clover about this, but he couldn't tell Clover what Ace looked like. Snake 'saw' Akane get thrown in the incinerator, heard him then (brings to mind a lot of questions about what Snake remembers that I guess come down to 'the loop is resolved and Akane doesn't die and Ace is a very sad man').
It's handwaved, but I think it's plausible.
Ace should remain suspicious though because obviously Clover will have her memories of the game dredged up in the same way as him. His only chance to kill Clover is in the Axe ending. Who knows who strikes first there, since Junpei dies while Ace is still at large? The real question is why he didn't go after Clover and Junpei in the Captain's Quarters, but that might've been really hard to cover up... Would've had to do the play dead trick.
And Ace kills basically everyone in some endings anyway just to keep his hands clean.
edit: oh, yeah, the fact that Snake never confronts Ace makes him paranoid Snake is working with Zero, so that should make Clover his next target if he knows that Clover is Snake's sibling. Which is why Clover dies in the Safe Ending, which Ace admits to. He only knows Clover is a big deal because she's related to Snake.
The note's main utility is for people to solve the decoy Snake murder, but I guess since this is a question I often see asked, I can't help but think how convenient it would be if it was more explicitly explained, and the note could easily serve as both a motive and an explanation. Then again, joining the dots that Ace and Snake were in the Gigantic together and Clover was in Q is about one step. Also, Ace would have destroyed the note or taken it with him.
So I guess there's no way the note can do both of those. Hmm. It's a pretty resolved question, I just haven't played 999 for a long time and these details stick out. :D