Its to drive oxygen out of the solution.

Well, the most common problem with reactions is oxygen, and it's the most abundant gas next to nitrogen in the air, so oxygen is most common.  However, bubbling (also called sparging) with an inert gas like nitrogen or argon serves to displace all dissolved gasses in a solvent with nitrogen or argon, which, for the most part, are hamless to reactions.  You can also look up a method called 'freeze-pump-thaw', which does the same thing.  But to answer your question directly, yes, carbon dioxide is also displaced.

And no, under normal conditions (like you'd have to make some REALLY strange conditions) nitrogen won't form ammonium ion.  However, you may see pH changes as the more liquid that you evaporate from solution, the more concentrated it gets, and thus the pH may change depending on the solution.