The equivalent to gwt.logging.popupHandler is now gwt.logging.hasWidgetsHandler. I think for the time being you could workaround your issue by using something like the following (untested) in your gwt.xml file:
<define-property name="gwt.logging.popupHandler" values="ENABLED, DISABLED"/>
<set-property name="gwt.logging.popupHandler" value="DISABLED" /> <!-- default -->
<set-property name="gwt.logging.popupHandler" value="ENABLED">
<when-property-is name="gwt.logging.hasWidgetsHandler" value="ENABLED" />
</set-property>
That way you could change your own gwt.xml files to use gwt.logging.hasWidgetsHandler if needed because that is what GWT will support in the future. However you still have the legacy gwt.logging.popupHandler property defined for libraries that haven't been updated yet.
Maybe GWT 2.7 could add such a snippet in its own gwt.xml file but in GWT 3.0 it will probably be removed again.
-- J.