Lost directories or indexes ??

I am running v2.1.0.1. My site is www.wevegotcomics.com . Yesterday, my site worked okay. I sell comics. My main categories are the 6 different time periods that comics were produced. If I click on a category that has nothing in it, I would get the Error 404 - Page Not Found. But when I clicked on a category that did have comics listed, it would go to that category and show the comics. Now, when I click on any category, I get the Error 404. This even happens on Subcategories that shows there are several comics listed. Right now, I have about 41 comics entered.

When I hover over the category, at the bottom of the screen, it shows that it is going to a directory with the same name as the category or sub-category, but upon looking at my file structure through cpanel, there are no directories with that name. I think that this is handled within the scripts.

How do I fix this? I'm not sure what happened between yesterday and today. Where do I start?

Thanks....