Of course it affects them. They hear boys taunting each other using phrases like that all the time, and they know what it means. Regardless of whether someone says it to them directly or not, hearing that tells that that their style of [running/throwing/fighting/whatever] is inferior to that of their male counterparts, and that further they will NEVER do it as well as a boy.
That said, this can be a useful motivator. I coach a girls' recreational volleyball team in the Spring and Fall, and while there are typically enough girls to fill out the league to six or eight teams, the number of boys that join the rec league for the sport is disappointingly low... typically they only get enough to fill one team.
The boys can mostly jump higher and hit/serve harder than the girls but at that age they have almost no control, so they shank the balls far more than their female counterparts, and often serve out of bounds. The girls regularly beat them because their serves and hits are still plenty hard in addition to being on-target and far more effective. Their teamwork is better too, and that's pretty vital in the sport.
After a time-out, the teams typically give a little cheer as they break the huddle and go back to their positions. Usually it's something like "ONE, TWO, THREE -- [TEAM NAME]!! " But one of my favorite things to do in these boys-girls games is to have the girls break huddle with "ONE, TWO, THREE -- HIT LIKE A GIRL!!!" The girls like the irony.
And yes, I recognize that I'm doing to the boys exactly what I don't want anyone doing to the girls. It's arguably worse since these boys are the only ones with enough love for the game to play what is (regionally at least) viewed as a "chicks' sport" and I may be crushing that out of them. But I do it anyway because I love the look on my girls' faces after they dismantle a boys' team.