There's no definitive answer, but for what it's worth, I've noticed a correlation between lower clickthrough rates and higher earnings per click on my site. When I made my AdSense ads less prominent and CTR slipped, EPC went up markedly. Why? Maybe it had something to do with available inventory for my site, or maybe it was because there were fewer accidental clicks and the clicks therefore converted better for advertisers. Who knows? We can only guess.
One thing we do know is that likelihood of conversion (as projected by Google's "smart pricing" formula) can have a direct impact on the actual price paid by the advertiser and--as a consequence--on the amount received by the publisher. As long as the clicks on your new site convert decently for advertisers (or seem likely to do so, according to Google's "black box"), you shouldn't have to worry too much about the quality or price of the AdSense ads displayed on the site.