Confluency or confluence, which term is correct to describe the % area covered by cells?
Searching Google Scholar for cell confluence returns 239000 hits, while searching for cell confluency returns 75000 hits. 

A look at the context in which they are used supports my gut feel, which is that

1:  "confluence" should be used in contexts of "% confluence"

2:  "confluency" should be used in contexts where you describe high or low levels of confluency.