Eurus used Molly Hooper to get to Sherlock.
And she succeeded. Eurus got on his nerves. She broke him mentally at that point, which led him to take his anger out of Molly’s so-called-coffin (he smashed it with his bare hands). She also said that “You didn’t win, you lost. Look what you did to her. Look what you did to yourself. All those complicated little emotions, I lost count. Emotional context, Sherlock, it destroys you every time.“
This means that Eurus saw Sherlock as an emotional person and that Molly was a weakness to him from Eurus’ POV. Eurus didn’t say anything spesifically about Molly’s emotions. She said “all those complicated little emotions”. She is directly telling Sherlock that he has emotions towards Molly and it complicates things (will also complicate things in the future).
That is absolutely what that scene meant in my opinion and I can say that: THIS SHIP HAS SAILED, THE THING I HAD BEEN WAITING FOR FOR 5-6 YEARS. I can finally find peace. Thank God.