How valuable are publications in lower-ranked conferences for MS admission applications?
When applying for grad school, the biggest thing is to demonstrate aptitude in research. You do not need to have a paper in a top-ranked conference to get into a good grad school. The fact that you have a conference paper is significant enough as it is. 

Will a top-ranked conference paper improve your chances over a paper in a lower-ranked conference? Yes, of course. But having a conference paper in a reputable conference should never hurt your standing.