yEd has always had a splash screen (what you call a "crap ad"). Showing the splash screen does not affect startup time in a noticeable way (after all the splash screen is just a PNG image and displaying a single image is essentially the fastest and most simple rendering operation there is).
That said, yEd startup time is fine in all of our tests. E.g. on an Intel i7 quad core with 3.4Ghz and a SSD hard drive running Ubuntu Linux with Java 8, startup time is 3 to 4 seconds. This suggests that the problem lies with your machines. Do you maybe have user-defined palette sections with lots of images?