Hi. I searched the app catalog and all I saw were apps that allow you to make PDFs from URLs, etc. I'm not sure what you mean by deleting PDFs, but if you don't get an answer here, maybe someone at Precentral.net can help.
I apologize but there is not an application to delete PDF files from the device directly.
You can connect your Palm Pre to your computer using the usb cable, and select USB Drive.
The Palm Pre should show up as a drive in My Computer.
You can then access the drive, and find the PDF file you want to remove and delete it.