I think it'd be nice (and give a more natural feeling to clipman) if the statusicon behaved like a toggle-button (or a menubar-menuitem). Since it's one of the few status/trayicons that you'd want to left-click, I think this makes sense.
@ochosi, since it is not possible to change the icon on a motion event (passing mouse over the icon), it's just not possible to fix this issue. @nick, what do you think about, should the notification area create an effect over the icons when hovering them with the mouse? Is that possible for you.
The panel only embeds remote windows, nothing I can do with them.
In this case maybe support Ubuntu's indicators? (i.e. if the indicator-plugin is present, behave like an indicator, otherwise use the statusicon. Examples of apps that do this are transmission, nm-applet etc.)
Closing as it is impossible to fix.