so, I just had a deeper just drop onto me from the surface in a flat area, take fall damage, and blow up my cobblestone generator. please explain why it's a WW2 Japanese pilot that ran out of ammo

That is absolutely normal sometimes. That is not a real issue.

I shall correct myself a bit, at the time of upload there is absolutely no information about the Deeper and it's spawning habits

They replace Creepers that spawn on stone/ores underground, your case just seems to have been an odd situation