there is no option to hide disabled accounts from the report since this would falsify it.
What you could do is generate the report in Excel format and then filter out permissions of disabled user accounts. You can find the tag for disabled accounts in the legend of the report.
yes it's possible. You have to set this "<Blacklists.AccountNotShowing.IsAllowed type="System.Boolean">true</Blacklists.AccountNotShowing.IsAllowed>" in your pnServer.config.xml. But it's a global setting. You can't set it on a per report basis. Except on the permission difference report.