Funny enough, deportation is regarded as a civil matter and thus the ex post facto clause does not apply here. Nothing in the constitution prevents the U.S. from deporting him to Antarctica. https://constitution.congress.gov/browse/essay/artI-S9-C3-3-...
Whether or not Superman is illegal or not, he is at least undocumented. And given the historical context and the authors, it's not a stretch to say that Superman is, in part, the story of a refugee trying to make it in America. Which is something than many people described as "illegal immigrants" identity with.