Suki is wearing full-face Kabuki makeup, so her lipstick doesn't seem out of place. When no other female characters are given excess pink around their lips (especially not Katara, and IIRC none of the incidental girls and women we've seen along the journey), lipstick stands out.

(It also stands out on the green-shirted pirate, but on him it is clearly meant as a joke. It's a joke in debatable taste, but a joke nonetheless. This makes it doubly hard for me to take lipstick seriously on Yue; I keep waiting for the punchline.)