Cleaning up a category list after removing products from a supplier is so easy... the Categories Admin page shows the number of products in the category. Grab the zero product categories and disable or delete them.
Is there a way to do that on product options? I have a LOT of size and color options that are no longer used or needed.
There isn't a feature like that for the options I'm afraid. You shouldn't be able to delete an option that is in use though - you will get a warning message with a button showing the product id of the parent product - don't know if that helps but should stop making mistakes in deletion.