There's no requirement to store models in module directories. Its up to the developer.
@sikkie: Yes HMVC controllers as partials.
But wait theres more...
Version 4.0.0 is a complete rewrite, faster and smaller, there is no need to use $this->load->module->whatever, anymore $this->load->normal works in modules just like is does elsewhere.
If you have a model in application/models the loader will find it and use it in your module also.
Version 4.0.0 is a few hours away yet. Thansk for your interest.