I noticed that both of them are used in many scientific papers. Are these two terms, or can they be used interchangeably?
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.
I have documented the history and current usage of the terms confluence and confluency in cell culture in an answer to another question specifically about the term confluency. As the current question has not been marked a duplicate of that one, and I believe the one answer posted to be incorrect, I am providing a brief answer here and direct the reader to my other answer for full supporting evidence.
Q. Are confluence and confluency two [different] terms, or can they be used interchangeably?
A. Confluence and confluency, as used in cell culture, have exactly the same meaning, and usage is a purely a matter of personal preference.
Confluence is a standard English word dating from the fifteenth century, and used as an abstract concept or applied to different phenomena in various fields. Confluency is a term almost exclusively used in relation to cell culture. In this respect, the definition from the short Wikipedia entry on confluency (sic) is pertinent:
In cell culture biology, confluence (sic) refers to the percentage of the surface of a culture dish that is covered by adherent cells. For example, 50 percent confluence means roughly half of the surface is covered, while 100 percent confluence means the surface is completely covered by the cells, and no more room is left for the cells to grow as a monolayer.
While there is no guarantee that this Wikipedia entry is correct, it reflects the fact that (1) since the 1960s some authors have used one term and other authors have used the other term to mean the same thing (2) that the same authors have used their preferred term in relation to both the concept itself (without any numerical qualification) and with a percentage qualifier.
I have inspected recent papers in the Journal of Cell Science (referenced in note (9) of my other answer and found that both usages, as above, are still current, as well as mixed usage of both the type prescribed by @MarchHo (confluency, but 50% confluence) and the opposite (confluence, but 50% confluency).
Both terms are accepted by all journals I have looked at, and I have failed to find a pronouncement on the topic by any standards organization or professional body.
Use whatever the people with whom you work use. If you are starting out on your own, make your choice depending on your attitude to the English language or the respect you have for a particular pioneer of cell culture. But, whatever you choose, never tell anyone else that they should do the same.