Are humans an ancient Kryptonian colony?

No. The timing is nice but it would not be sufficient to explain why Humans (Homo Sapiens Sapiens) and Kryptonians (Homo Sapiens Kryptonus) resemble each other in such a spectacular fashion externally.

• The problem lies in the fact that Kryptonians would all have had superhuman abilities unless whatever it is that gives them their powers under a yellow sun was a recent addition to their genome.

• Despite their superhuman abilities, all of the Kryptonians who lived on Earth 18,000 years ago still managed to die out. However, they could have been the source of many of the superhuman myths of ancient times if their genetics were somehow compatible or transferable.

• Nor has DC made it apparent whether the Human genome and the Kryptonian genome are compatible in this new release of the Superman mythos. If they decided that it was, this could explain superhuman potential within the human genome quite nicely. It would be sporadic but when it surfaced, the potential for superhuman ability could spontaneously appear (as it seems to do in the comic DC Universe).

However, it might be an explanation for the later appearance of Supergirl...

Not according to the official prequel comic.

_{Which you might be able to read here.}

In the prequel comic, the ship that landed in ice was actually Kara Zor-El's colonisation ship - it was meant to go to a different planet, as a part of Kryptonian expansion effort.

It was sabotaged by a guy named Dev-Em, who was sentenced to death, but managed to escape on Kara's ship with help from some people from the Kryptonian council. He murdered Kara's crew, but left her alive (they were all in cryo sleep pods). After 10 years they arrived to the Solar System - Kara awoke, discovered what happened, they fought, damaged the ship, it crashed.

It's implied that they indeed crashed only (geologically) recently, certainly not enough to be Homo Sapiens' ancestors.

_{Click for full resolution.}