This is highly subjective - but if your dict is getting to be more than 2-n deep, I would revert to creating a class and defining methods/properties to do what you want.
I think your end goal would be to create a "multi-column" data structure so you can store any number of attributes for a particular object (in this case, a site). Creating a site class would accomplish that and then you can stick instances wherever you would any other object (variable) - with some noted exceptions.
