I just want to make sure I'm understanding the problem...
You can find the podcasts on the iPod. You find them by going through the "genre" path. So it's probably something like Music -> Genre -> iTunes U on the iPod's screen.
You manage content on the iPod manually, which means you drag content to the iPod in iTunes. You don't use the Sync button to load content. This also means that content on the iPod right now does NOT necessarily have to be in the iTunes library. If you automatically sync, then all content on the iPod must also be in your iTunes library, but not if you manually manage content.
With that in mind, if you are searching for the iTunes U content in your iTunes library, it may not be there. That might explain why your searches come up empty.
To find the iTunes U content on the iPod (using iTunes), select the iPod in the iTunes sidebar, and drop down the iTunes media categories (indented UNDER the iPod). If the path for finding iTunes U content (on the iPod) is
Music -> Genre -> iTunes U
click on Music indented under the iPod. Over to the right, sort the list by Genre. See if iTunes U is there; if you are sorting by Genre, they should all be grouped together. If you find them, you can delete them from that list. Select the item and hit the Delete key. You can select multiple items at once.
You are managing content manually, so deleting an item there deletes it from the iPod.