One primary site and several secondary sites. Is it possible to assign a group of users only the permission to run and view reports against clients within their secondary site or for a specific collection (which includes only clients from a specific site) ? And if yes, how ?

Depending upon whether you are using classic reporting (.asp reports) or SRS reporting, the exact steps to make that happen will be different.However, the answer is essentially the same, you could do so by creating custom reports for each group, where you, within the customization of the report, i.e. the "where" clause, pre-apply a filter to filter the reports to only that group's clients.Standardize. Simplify. Automate.