If you can show us a sample for both, 2 and 3 columns, then that will help to see which will have higher CTR
2 column: http://www.wpthemesfree.com/view.php?theme_id=2239 3 column: http://www.wpthemesfree.com/view.php?theme_id=1338 If you want sample, that means that CTR does not affected by the number of columns? So which do you think have higher CTR
I think 3 column is more better they provide you good space to display visible adsense ads .But their are many two column blogs too which have placeds adsense ads between post very nicely .
It doesn't really matter what kind of template layouts you use for your blogs. It is how you place and optimize your Google AdSense Ads that matters most. You have to play around with your ads placements and see what work best for you. Nobody has the same results, there are too many factors that affect CTRs anyway. It took me 6 months to find the best Google AdSense ads placements that generate high CTRs for my blogs!
Two columns have always given me better CTR if that is what you want to know. Three columns is when you have a lot of information to show on the Home page which only means more and more links for the visitors to click that competes with the google ads for clicks...