This approach solved the same problem in my workflow:

I use linked Smart Clips with nested Layer Comps for every section. For instance, create a Smart Clip for the header section with Layer Comps like home, mouse over, active etc. You can select the required Layer Comp of the linked Smart Clip using the properties panel for every Layer Comp of the main document. That way you can have many states separated in many files with a rather flat main structure.

Sorry, this sounds a bit weird, but I hope this helps in some way.

This approach solved the same problem in my workflow:

Layer comps in Smart Objects

I use linked Smart Clips with nested Layer Comps for every section. For instance, create a Smart Clip for the header section with Layer Comps like home, mouse over, active etc. You can select the required Layer Comp of the linked Smart Clip using the properties panel for every Layer Comp of the main document. That way you can have many states separated in many files with a rather flat main structure.

Sorry, this sounds a bit weird, but I hope this helps in some way.

Additional Info: Adobe Help – Layer comps in Smart Objects