His mother was Pauline nee Eckmann, and his father was Anthony.
Europeans don't play with names nearly as much as English speakers do. The kind of thing you're describing is pretty much unique to English speakers, who have a long, long history of doing all sorts of things with names, and words in general, just for $hits and giggles. So your "contraction" theory, though plausible in an English speaking country, is way outside the norm on the continent.
Like John, I'm inclined to view it as either a clerical error or, perhaps, an actual variation based on Apolinary. It was a fashionable name in Catholic countries the 1800s. This is by far the most plausible explanation.
Also, the "au" Pauline sounds like the "o" in Apollonaris only to many, but not all, modern Americans. This is called the caught/cot merger in linguistics, and didn't become widespread in American English until quite recently. Before then, and for many Americans still, they were pronounced quite differently. Outside of modern American English, they are pronounced so differently that a pun of the sort you are proposing is very implausible. They are pronounced completely differently in Polish.