Java works with 72dpi. I.e. at zoom factor 1, node size of 90 x 90 in yEd will result in printout size of 1.25in x 1.25in and yEd grid distance of 90 will result in printout grid distance of 1.25in.
In this context, the zoom factor is determined by settings "Scaling" and "Scaling Factor" in yEd's print options: