That doesn't make sense. Atheists could possibly outnumber Catholics in your country. The point to conducting a census is to insure groups aren't under represented.
I imagine Catholics would be outraged if there wasn't a box for them to check off.
How does it not make sense for the people in power to try to remain as powerful as possible?
The point of conducting a census is to provide information for the government (and others) to act upon; What actions the government chooses to take is determined by the opinions of the people in power, not by the information they use in making those decisions.
It's a representative democracy, and it's dominated by two parties. Neither party has anything to gain from throwing out policies that are supported by their caucus, in an attempt to attract a voting bloc that is by definition unpredictable and non-homogeneous. Espousing causes that are opposed by the Catholic church is likely to lose you the votes of Catholics; But it is far from guaranteed to attract any votes from Atheists, who are more likely to be interested in other policy areas. Atheists are not a united bloc.
Look at the way politicians behave in regard to other tribalistic issues - say, sports. Politicians on both sides of the chamber wave the green and gold flags whenever an Australian sports team plays a major match, particularly if they play against a hated rival. Supporting the Wallabies when they play the All Blacks is a 'no lose' proposition for an Australian politician. Of course, lots of Australian voters don't give a rats arse about Rugby Union - but trying to appeal to the 'No Rugby' demographic gains you a tiny number of votes (if any), while costing you the much larger number of votes of those who think Rugby is vitally important, and who are INCENSED that you didn't support their team.
Some voters will say "I am not voting for him, he didn't support the Wallabies" or "I like him, he supports the Wallabies". But nobody says "I'm going to vote for him, because he shares my lack of interest in Rugby".
It's the same with religion - believers are fanatical, and like footy fans, will change their allegiance based on a perceived lack of support for their beliefs. But non-believers are (by definition) apathetic, and will only consider specific policy measures, each on its merits. That's not a level of support that a politician will stick his or her neck out over.