Hello, I have the same anoying problem, and I've just find the solution.
First you need to have a soft like Podworks (there must be other that have the same function), in order to locate on the iPod disk, the right location of the files (podcast or music), you want to delete. With Podworks, you just have to select the podcast you want to delete and go on the Information icon (I), it give you the write location, that you should start like this : iPod_Control/Music/...
So you note that or have Podworks open, while you look in a finder window to locate those file on the iPod.
But You'll tell me : on the finder window of the iPod, you don't see the folder iPod_Control.
It's normal, it an invisible folder.
So to make it visible, you have to go to the Terminal (in the folder Application utilities).
When you double click on terminal, you write or copy/paste the following instruction : defaults write com.apple.Finder AppleShowAllFiles true
You press enter, and the you have to restart your Finder, for that you go into the apple menu
(left up corner of the screen), and go to the "force to quit" menu.
Then when your desktop is back, if you open your iPod, you'll seen many more folders, their color is fade, but you can open it, and you'll find the location that Podworks have tell you before.
Then you just have to throw to the garbage the files you want, and empty the garbage in order to delete the files completely from your iPod.
It's seems a little long and special, but if you know a little Mac, you'll find it really easy.
And it works well.
Hope you understand (pardon my english, but I'm French...), if not ask explanation, I'll try to detail more.
Bye and take care.
Phil