[JWait]

Ok, it looks like "accessories", 'apparel", and "performance parts" are "root" categories, as well as "home". A question, "home appears to have 107 sub-categories, and "performance parts" appears to have 240.

A little check reveals that 4-Stroke Leak Down Tester - SKU: SKU17364 is in
GPmotoparts :: Home :: Performance Parts :: Tools :: Testers, Tuners, Gauges & Adapters
as well as
GPmotoparts :: Home :: Performance Parts :: Tools :: Testers, Tuners, Gauges & Adapters :: Motion Pro

Is there any reason for that? What I am getting at is it looks like a lot of your products may be in for instance the "performance parts" category, and also in the "home/performance parts" subcategory. Does "home have subcategories named "accessories", 'apparel", and "performance parts", and if so, do those subcategories have the same subcategories as the "root" "accessories", 'apparel", and "performance parts" categories? It looks like for each product, the "additional categories" section lists a subcategory of "home" that has the same name as the category the product is in as the main category. Another possibility is you have duplicate products with the same name and different sku's (SKU: SKU17364 and SKU: 17364 are not the same), and yet another possibility is that somehow your products pages and your manufacturer's pages got combined. What a mess!

What happens if you go to admin - modules and uncheck "manufacturers"? You will probably need to clear the templates cache before you get a different result (admin - summary - tools - clear templates cache is a little over half way down the page).

To answer your original question "Hiding main categories" go to admin - general settings - general options and look for "If ticked, the categories list always shows root categories:"