With occasional oblique references to Kryptonians having travelled to other planets in the distant past, is there any connection between the Gods and Goddesses of mythology and empowered Kryptonians in the DC canon?
Certainly not all of them. Some, perhaps. It's worth noting that the Kryptonians were not the only pre-human-history spacefarers in the DCU pre-New-52; it is unlikely they are in the new-52, either.
We also know that some of the Greek pantheon are in fact still present - Wonder Woman and her fellow Amazons have had encounters with the Greek Gods, and they aren't Kryptonians. They are in fact more powerful than Kryptonians. This is true in the Silver Age, Bronze Age, Modern Age, and New 52 comics.
Likewise, several of the Egyptian deities are also known (again from the Wonder Woman comics).