I think it'd be pretty cool if the thing Kobra found on the ocean floor in the Justice League part of Batman Beyond Unlimited was the Midgard Serpent. It's usually sleeping somewhere on the ocean floor, yes?
Why not? It's a giant snake. It's supposed to arrive during Ragnarok, the end of worlds, and that's what Kobra is striving for. And it'd be fun. The Justice League vs. the Midgard Serpent. Tell me you don't want to see Big Barda trying to kill the Midgard Serpent. You know you do.
Sure, Kobra worships Kali-Yuga, which is a completely different set of deities, but fanatical organizations dedicated to ending the world can't be so hidebound. Besides, no one would expect it, and it at least works within their snake motif.