I guess what you are saying is that correlation does not imply causation, and in this case the causality arrow may go the other way round.

In this case, there's something that actually can help establish the direction of the causality arrow: time. If the citations precede the downloads, then sure, it's more well known papers get downloaded more. This papers show that the downloads precede citations though:

"number of downloads from Sci-hub was a robust predictor of future citations"

While it's not a watertight argument that downloads lead to citations, the theory is at least plausible.