Thanks for the complete answer!
I also have an old site with around 1000 posts and also around 4000 products and just use categories. It is quite difficult to arrange everything and I was wondering how do you do it.
In fact you just have categories in sidebar and then "sections" in the main menu so user can nav in your site.
As I see it, the important thing is usability and easing the navigation. "urls" dont mind so much.
Thanks again