No it's not a problem.
It's only problem when you fill the screen with tons of overlapping quads and have to fill them all. Even better hardware can have some problem, because fill rate is not really raising that rapidly. But then again, it does not really matter whether or not they are transparent. Because of this, often simple quads are not always used (more complex shapes can be more useful because of lower fill rate required) or they are optimized/rotated to reduce transparent areas to minimum.
HOWEVER, in Fonline you are not going to see huge splats covering whole your screen, with smoke and fire all over the place. Perhaps at massive zooming, but that's not the thing that requires huge attention.
If those splats do not exist yet, it's more likely because there are no inbuilt particle generators or that kind of stuff, and artists have to incorporate them within the model which takes far more time and work. Performance is not problem here.