Because Varys doesn't control the Little Birds in Westeros or at least King's Landing anymore, when he fled to Essos, Qyburn took over control of them.
LITTLE BIRD: Will Lord Varys ever come back?
QYBURN: I don’t think so. Do you miss him?
LITTLE BIRD: He was nice.
ARTHUR: He called us his little birds. He gave us sweets.
QYBURN: It’s funny you should mention that. Guess what I happened to find today. Candied plums from Dorne.
QYBURN: Now remember, if any of your friends like sweets or need help, they can always come to me. All I need in return are whispers.
CERSEI: Varys's little birds?
QYBURN: Your little birds now, your Grace.
Game of Thrones, Season 6 Episode 3, "Oathbreaker"
On top of this who's to say he didn't know about the scorpions at King's Landing? In fact the evidence states he probably did know considering they placed Drogon further back than the main forces when they went to demand for the release of Missandei.