There hasn’t been any hint otherwise. There was a storyline where his father Jor El turned out to be alive (and kind of a dick) and took Jon on a trip to space (which, through space-time fuckery, resulted in him aging to a teenager while his childhood friend remained the same age). Jor El seemed satisfied that Jon was his biological grandson. Batman was apparently involved at various points to help out during the pregnancy and in the years since, and he never gave any hint that the kid was anything but Clark’s. None of the DNA-obsessed villains have brought it up.
Until some editor decides to undo everything, we’re supposed to just assume it’s all as it appears.
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