I've always assumed the sites they track lead to some serious small sample biases in certain countries. It's an Irish company, so I'd guess most of their sites are European language based and wouldn't be surprised if there's a high amount of tech sites.
For example, it wouldn't be that surprising if they got data from HN, or a similar site. What portion of Indian desktop hits to this site do you think report using Linux?
Statcounter data is based on website visits. It is very unlikely that any significant fraction of them are being used for browsing web, or even have a graphical interface with web browser installed for doing it.
I wonder whether that's real or a mirage caused by Linux servers masquerading as desktops.