Clark took Lois there for their 50th wedding anniversary, which would have been in 2046. He'd also been to Luna City 30 years ago for something else. I'm quite sure there would be plenty of ways to get rid of those thumb prints over the years, even if they keep the records for that long, and besides, who says he stayed at the Luna Hilton that time? There would probably be a division of the Superman Foundation that routinely took records of trips and erased the prints of their long-lived members from computer records.
Nan