Well, they don't print cards using the template Kill Card 2 has anymore. Now it would say "Until end of turn, target creature becomes a black Germ with base power and toughness 0/0". See Turn to Frog. Not sure if you want it to lose all abilities too, but Turn to Frog is close enough to serve as an example.
This is because it is clearer and the effects are identical. So, no, there are no differences with your above cards in layer 7. Obviously Kill Card 2 applies in Layer 4 as well to change the creature type, but that doesn't affect the 0/0 portion of the effect.
Kill Card 1 (Uncommon)
3B
Instant
Until end of turn, target creature has base power and toughness 0/0.
Kill Card 2 (Uncommon)
3B
Instant
Target creature becomes a 0/0 black Germ until end of turn.
This is because it is clearer and the effects are identical. So, no, there are no differences with your above cards in layer 7. Obviously Kill Card 2 applies in Layer 4 as well to change the creature type, but that doesn't affect the 0/0 portion of the effect.