I would need a few more details about your plan before I could answer your question directly!

However, in general, if you're using categories with discipline, and you don't have too many of them, then having them in the main menu may help visitors. If you have product landing pages, though, these could also go into the menu and you don't want the nav bar to become to cluttered.

So the important thing is not to think about the search engines, but to think about how to make it as easy as possible for *humans* to find the important pages on your site.

This article may help, because it describes how WordPress categories (and tags) work and offers some SEO tips at the end:

Optimise WordPress with Categories and Tags | WealthyDragon

Cheers,

Martin.

Thanks Abledragon!