No, there is no way to query the Viewpoint server's database directly. All access to the data today is through Java APIs that are part of the PDK.
However the majority of portlets do offer the export feature so that any information displayed in the portlet can be pulled out of Viewpoint. The export for the metrics portlets (Capacity Heatmap, Metrics Graph, Metrics Analysis, Viewpoint monitoring) was introduced with the Viewpoint 14.01 release. So you should be able to get the information you want.
Metrics Analysis allows for multiple metrics within a single system or across multiple systems to be viewed in a single portlet view. As such, the export of a Metrics Analysis fully populated metrics display will act as a lump sum of all those metrics in that view via a single operation.
Is it still possible to create custom portlets utilizing the PDK @stever mentioned, that can leverage the viewpoint UI framework but query organization specific data tables?