Two Modules should be split into different structures in your foundation layer. However they can definitely reference each other.
http://helix.sitecore.net/principles/architecture-principles/layers.html#foundation-layer
Unlike the Feature layer, there is no strict convention on
dependencies between modules in the Foundation layer. This means that
one Foundation layer module can depend on another Foundation layer
module in the solution – as long as they rely on the basic principles
on component architecture such as the Acyclic Dependencies Principle
and the Stable Abstractions Principle:
Keep in mind the rule basically states that dependencies from a current module should always be more stable than the current module. Having said all that, you asked specifically about where to place this module and the namespacing. I'd recommend not placing it in the same folder as another module, since if it really is another module than it should have clear separation. But that is just my opinion, Helix on the other hand doesn't include this, and there is nothing that says you can't do that.
But if you are considering placing them in the same folder as the other module. I question if it really is another Module or just another project that's part of the existing Tagging module. It's hard to make that determination based on the details provided, but you should consider if it really belongs as another module.
