Obscuring Simulink subsystem names might not be possible, but you can strengthen model protection by converting the subsystem (whose content you intend to protect) in a Referenced Model http://in.mathworks.com/help/simulink/ug/overview-of-model-referencing.html?searchHighlight=model%20referencing and then enabling protection.
You can have a look at the following documentation which shows the steps how to do it:
This short video (link given below) also nicely demonstrates how model protection can be enabled and how the Intellectual Property of a model can be protected:
Hope this helps!
Cheers,
Debarati
