I know Canons have a shot buffer, but relying on this with larger fine high quality shot saves whilst the camera software is working hard and Ultimate is deleting a file seems too chancy?
FWIW, all these cameras write the file pretty much immediately, I don't think buffering is a factor. As long as the script uses a reasonable threshold to start deleting, I wouldn't expect any problems deleting files between shots in an intervalometer. Deleting, by itself, takes negligible time.
The only problem I'm aware of with deleting is some cameras (newer than your A560) crash if you delete images in record mode and then try to switch to playback or shutdown. For a script like ultimate, one way to work around this is to overwrite the existing files with 0 byte placeholders and delete them after switching to play.