It could still be a pimple even if there appears to be no hair there. After all, girls get pimples on their faces even though there isn't really any hair there. We still have tiny hair follicles and pores that can get clogged over our whole body even if you don't see any hair there.
It is possible that she is getting a vaccine then. I do not know a whole lot about STD vaccines, but I believe the FDA approved an HPV vaccine about a year and a half ago.
I understand why you would be curious, confused, and concerned, but why not ask her? She would know exactly what she is getting shot for and why better than we would. Communication is pretty important in relationships, especially when you're dealing with sex and possible STDs. Some of that can be life or death stuff. If she tells you exactly what she is getting and why, then you could even ask her to bring home a pamphlet from the doctor or look it up on the internet if you want to know more about it.