There is no way that I know of that they can be deleted directly from iCloud, but you are welcome to look around. You access iCloud directly by going to icloud.com in a web browser on a computer. There are no syncing controls there, just apps and files.
Let's try a slightly different approach.
Sign out of iCloud on all but one device, including your PC. I'm not familiar with Windows, but I understand there should be a control panel for iCloud syncing. There is nothing on the Mac that lets you turn off just keyboard syncing, but maybe there is on Windows.
Pick the most important device to 'not' sign out. Signing out then back into iCloud can cause some snafu's and might require enabling it again in individual apps. Let's minimize that.
Delete the shortcuts on all devices, including the one that is still signed in. If you can, let things ride for a couple days and see if they still come back on any of the devices. Note which if any they come back on. That might come in handy later.
If they do not come back on the signed in device, sign back in on each device one at a time, and wait between however long you can. Save the PC for last. Lets see if we can narrow down the device causing the problem, if the root cause is a device or the computer. If the root cause is iCloud, the shortcuts will probably come back while you are still using one device.
I hope this works, or at least offers some more clues.
Good luck.