Thanks to Swpalmer and Ken for the clarification!
I’ve checked the JOGL User’s Guide and think it’s well understandable now. Thanks a lot.
So … because my game will mainly be startet via JAR clicking I’ll continue to use the setProperty inside the main class but also add these settings to the Webstart script. So it should work with both starting methods.
Great; another problem solved. 
P.S. I love the new VSync control method setSwapInterval(1 | 0). It’s very valuable for 2d looking JOGL games.