Did Varys not notice Littlefinger’s massive embezzlement or did he deliberately keep quiet about it? Revealing it would probably have been in Varys’ interest as Littlefinger’s schemes bring chaos to the Realm and they complicate or unravel Varys’s own plans plus the embezzlement is genuinely bad for the Realm no matter who sits on the Iron Throne.

To the contrary, Littlefinger’s embezzlement weakens the Baratheon dynasty. By allowing it to continue, Varys allows Littlefinger to do his dirty work for him, and can reveal the truth whenever he wants. 

Once Varys takes over, it would be pretty easy for him to reveal the truth about Littlefinger’s treason, declare his assets forfeit, and renegotiate the debt on good terms.