There's nothing currently built in to CI or HMVC for this.
I prefer not to reference files that are allowed direct access, like images/js/css, from within the application directory. Mainly because:
I don't want anyone to know what the guts of my app look like. By referencing files from directly within a module, you expose your application's directory structure.
I would never do this if I weren't using HMVC
You must now allow direct access to (certain) directories within the application via .htaccess. For security reasons, I prefer to simply disallow the entire thing.
I understand the desire to be as modular as possible, but to me it's not worth this hassle. I prefer to keep a separate directory in a public folder called "modules" (duplicating my application/modules structure), that has nothing but "assets" (css, js, images...).
I'd offer some code but I have no clue how you are adding js/css to your views - it's probably much different than the way I do it. It would be easy enough to write a function to detect the current module, controller, or method and change the asset folder automatically, but this may interfere with other shared assets. I'd suggest writing an entirely separate function for loading assets from modules.