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This is a tricky question that we honestly don't know much about.
Who says thresh doesn't see it?
I kinda answered this in my other comment: My interpretation is similar, it's not that he doesn't "see", it's that the seeing has no effect because his level-up condition is silenced.
Silenced Yi ain't gonna level up will he?
No, silenced champions will not level up. However, the only Silence card that can target champions is Hush, which only lasts for one round. After that, he will gain progress even from when he was silenced and level up. It's still a card with the name "Master Yi" that dealt damage, so it counts for the global condition. It's just prevented from affecting the current copy while it's silenced.
Edit: Added link.
Wow, well done LordRedStone_Nr1! I think you nailed it - silence champions don't "see", so that is difference OP's text (silence will affect it) and the current text (won't be affected).