Hi everyone,
I had the same issue as everyone since iphone 5 was released. I think i might have found a solution as my deleted shortcuts have not returned so far, keeping my fingers crossed, since I tried this method.
Assumptions, you have
1) multiple Apple devices sharing the same apple id.
2) iCloud turn on on all devices
Here's how we clean things up once and for all!
1) Gather all your iOS devices together
2) Restart all your devices
2) Go to Settings>General>Keyboard>Shortcuts
3) You might see different devices having different shortcuts entries or they could all be the same since they are synced through icloud.
4) To delete the unwanted shortcuts, you need to delete them on all the devices (i have 2) as fast as you could. Why?
My conclusion is, iCloud or the syncing process is not intelligent enough to know which "master" instruction to follow as there are a few devices using the same apple id and connected together. So if you have 2 devices, if you delete a shortcut from one device and not from the other, icloud could have checked all devices and automatically keep the record that has more information instead of telling the other devices to remove the entry.
5) Once you are done deleting the unwanted shortcuts, restart your devices again. Enable your data connection or wifi as they should be connected to icloud. Why? Because I noticed every time when I restart my devices, they seemed to "talk" to icloud and update whatever is on icloud with them. You would have succeeded if the updated shortcuts didn't show up the first few minutes that you have restarted. Otherwise, your unwanted shortcuts would have reappeared on your devices. Try again! Good luck!
I'll update if my unwanted shortcuts return!!! Keeping my fingers crossed!!!