Currently, the module suite project type does not work for "Inspect & Transform". So, you need to open the modules within the suite and then the classes within the module will be found. Should be possible to apply any of the refactorings from "Inspect & Transform" to a complete module suite (i.e., NetBeans Platform application) project.
*** This bug has been marked as a duplicate of bug 201127 ***
Is this really a duplicate? Bug #201127 is merely about adding something to the context menu of NBM projects which is already available in the main menu, as a convenience; whereas this issue seems to be a request to invoke the action (whether by context menu or main menu) on a suite project and for the refactoring infrastructure to treat it as a container - I suppose by setting the scope to all subprojects. Which seems like a bad idea to me (WONTFIX), since we do not generally have actions operate on (possibly nonopen) subprojects.