You can delete only self-signed digital IDs that you created in Acrobat.
I know it's been a long time since you posted your question, but if you are still interested here is what you need to do.
- Launch Internet Explorer
- Select Tools > Internet Options (you can get to Tools either from the menu, the toolbar button or Alt+X)
- Select the Content tab on the Internet Options dialog
- Click the Certificates button in the middle of the Contents panel
- Select the Personal tab on the Certificates dialog (it's usually selected by default)
- --Before continuing I'd recommend exporting the digital IDs to a file in case you ever need to get an old one back again)--
- Highlight one or more digital ID(s) and then click the Remove button
The next time you launch Acrobat and go back to the Security Settings dialog the digital IDs will be gone.