Possibly but does it realistically matter? I don't care why my games run on linux I just care that they do. I encountered a few cases where the native version was inferior to the wine version (Cronos is one example). With wine improving there is very little downside to just using it.

short term yeah, probably hurts native ports since "why bother". Long term though if the market share for Linux is particularly high I could see more native development.

Either way my comment is intended as more humorous than truly insightful or prophetic.