Re SmartGitHg:
SmartGitHg does not seem to be a good example. It does not seem to be open-source, so there is no way to determine how SmartGitHg specifies the application icon. However, even if SmartGitHg was open-source, that would not help either because it uses SWT (a native GUI toolkit) instead of Swing (Java's cross-platform GUI toolkit). So, SmartGitHg is really not comparable to yEd with regards to handling application icons.
Moreover, SmartGitHg's desktop file conceptually differs from yEd's desktop file: SmartGitHg specifies an absolute icon path Icon=/opt/smartgithg/bin/smartgithg-256.png while yEd specifies a relativ icon path Icon=yed. Unfortunately, I know much too little about Linux desktop configuration to know which approach is correct/recommended.
Re correct icon location:
Well, yEd's PKGBUILD script specifies ${pkgdir}/usr/share/pixmaps/yed.png as destination for the application icon.
troffel, can you verify that ${pkgdir}/usr/share/pixmaps/ is the only directory with a yEd icon on your system? E.g. run find /usr/share/icons/ -type f -name "yed.*" to check the /usr/share/icons directory for yEd icons.