If no existing tools have that feature, you could try something like Padre, which have this feature in their TODO list. I don't think it's done yet, but maybe you could help/encourage them to work on that feature next?
Parsing Perl files located in subdirectories of a particular directory might be fairly straightforward (with the caveat that only perl can parse Perl): you can find Perl files using File::Find, and then parse them with adamk's excellent PPI. Visualizing it and plugging it into Padre will be the (only!) hard bits.