NHRA does indeed have a classification for the '69 L-89 Novas, for BOTH stock & superstock. But, if you know very much about NHRA then you know NOT to base your argument on anything they do or don't do!
And I can see both sides of the engine stamping argument. On one hand, things such as head gaskets and head bolt torques are different between the L-78 and L-89. But on the other hand, the Nova/Camaro did share rear-end codes, as Marlin stated. I would tend to think they would have used a different code, but what do I know?!
As for the *why* behind the L-89...