After some investigation, this problem turned out to be an error in Oracle's Java Runtime Environment versions 7 and 8 for Mac OSX. They have been made aware of the problem, but seem to have implemented an incomplete fix (the corresponding error report [macosx] apple.laf.useScreenMenuBar regression comparing with jdk6 is marked as "fixed").
Unfortunately, the only workaround/solution I have found is running yEd on Apple's old Java 6 instead of Oracle's newer Java 7 or 8.