This is still a problem in 2016. Now most of the Notebooks have Hi-DPI/retina displays, all major operating systems set high DPI values. I know this is problem in Java UI but other applications (Eclipse, IntelliJ, ...) did manage to achieve it. In a tool like yed I think this support is even more critical.
I'm on Linux, GNOME3. HiDPI-Scaling set to 2x. Most/99% of the applications scale well, yed does not.