Madoka seems to waffle a bit on the answer to this one. Because the truth is that she definitely still is upset on the inside to see people go - and it's strong enough that she can't always contain it and smile, really. In fact, it's often that she can't. Even right now it's pretty hard.

But she doesn't want to say it out loud. Mostly since she doesn't want to bother him or anyone else with it.

Hence why she doesn't remark anything about it. Instead, as she looks up at him with those big eyes of hers, she asks: "Would you not feel sad if I left, mister Yondu?"