Adoption laws are very different in 2006 from what they were in 1965. I would bet the adoption is legal.
Even though there are indications that it was done differently in
Lois and Clark (and in
Smallville for that matter) it is my pet theory that Clark's adoption was perfectly legal. If Martha and Jonathan declared Clark a foundling (which he techinically was) and adopted him as such (there are specific legal steps in getting foundlings birth certificates and Social Security Numbers) then there is no question about his citizenship in my mind. So perhaps there would be some suspicion from Bureau 39 concerning a foundling and the ship they had, but as I said this is my pet theory and so I choose to ignore Bureau 39.
As to the matter of Superman's citizenship-- Wendy Richards has a
brilliant story
Green Card which explores the question of Superman's citizenship.
I read another one that recently (I can't remember who it was by) that had Trask trying to kill Superman and claiming he was an illegal alien and the Secret Service showing up and stopping Trask and saying that Superman had been declared a citizen during Reagan's (or was it Nixon's?) administration.
