If I understand the question correctly, you are adding a path to an include folder but the subfolders are not being traversed. Indeed, you have to explicitly add paths to all folders in your Polyspace project.
If you set up a project in the Polyspace user interface, during project setup, there is a check box Add recursively that automatically adds paths to a subfolder if you provide the path to a top level folder (see image below).
If you are running analysis at the command line, you have to add a -I to every subfolder. You can write a script to generate -I's to a subfolder given a top level folder, or set up a project in the Polyspace user interface using the above convenient check box and generate an options file for runs at the command line.
