Well since Hubpages integrated their new feature,so getting less adsense earnings is not abnormal. I recommend you to turn on your Hubpages ad program if you are yet to join the Program.
The majority of the Adsense revenues goes to the Ad program (also from premium advertising network) , which Hubpages distributes to it's user based on the page impressions.
If you are using only adsnese, your click ratio should not decrease in number I guess. But it's better to use Hubpages ad program and Adsense both , but your Adsense earnings will be significantly lower.