Yes, the singleton will be respected.
Say you have com.foo.Singleton.class and it only exists in jar singleton.jar. So long as there is only one module Mx that includes singleton.jar in its <resources> element, there will only be one classloader that defines a class named com.foo.Singleton.
Other modules that add a dependency on Mx only declare that they want to have access to whatever classes Mx exposes; they aren't declaring that they can be a defining classloader for the bits described in Mx's <resources> element.