Steven,

Not exactly what you mean about the multiple categories…do you mean can products fall under more than one category? If that's the case, then yes they can. By default the category structure is products —> subcategories, with all product items falling under the parent category of products. Products can still fall under more than one category, and if you don't want to be forced to use products as the parent category for all of your items, you can get around it simply by changing a couple lines here and there in the theme files.

As for WPMU, it seems to me like your question is geared more towards the advantages of WPMU over Wordpress? The benefit of the theme itself is that it is compatable with WPMU, but if you do not plan to have your own hosted storefronts for visitors, there is no need for you to use WPMU.

Yes - you change one line of code on the hompage and one line of code in the storefront.php (assuming you'll be creating a grid storefront page and using the supplied storefront grid template included with the theme). All it requires is adding a comma and the additional category names and/or id numbers of each main parent category.