As I understand it, it will show that the eMail was "opened" because the tiny little image mail providers use to track open rates will be downloaded on Apple's server. So, eMails will show as having been opened regardless of whether the subscriber actually opened them.
As far as I can tell, it shouldn't affect clicks because Apple is only downloading images not following links in the eMail.
So, basically, it just means open rates are as much a meaningless statistic as they were before. Previously, if people had their eMail apps set to not download images, or if they did not use HTML mail, they would have not shown as having opened their eMail even though they had. So, before, actual open rates could be higher than reported open rates, now reported open rates may be higher than actual open rates.
Bottom line is don't trust open rates.