If you really wanted to verify that the injector is shut off, you can look at the signal through an oscilloscope. This is what an injector pulse looks like:
When I was a senior in college, I developed a microprocessor application that functioned like the MPGuino. This software read the length of an injector pulse, and was very precise. From this signal length, and the injector rating, you can calculate how much fuel is used. If an MPGuino is reading 9999, it's because it's not picking up a length for the injector pulse, and therefore assumes no fuel is being used. It's quite possible that the amount of fuel is so tiny that the MPGuino reads 9999 but you might actually be using some fuel, but it would be so little that you could consider it to be no fuel.
Also, my Honda manual confirms that DFCO exists under certain conditions. I don't think the manufacturer would call it fuel cut off if it wasn't actually cutting off fuel.