I recently took over a site that is just so scrambled, refering to the PHP code, that Studio actually chokes when adding that site to a project. This is due to Studio scanning every page to add the functions, variables and classes to the project pane.
If this is the case with you, currently there's no way around it other than to not use the project feature with that site. Just use the filesystem pane to navigate and you should have a pretty decent response time.
The site I refer to has about 100 functions and about 50% of them are redundant functions but with with different names -- therefore just taking space.