It's been a well-known fact that using native VirtualBox or VMWare shared folders is a terrible idea if you're developing a Drupal site (or some other site that uses thousands of files in hundreds of folders). The most common recommendation is to switch to NFS for shared folders.
NFS shared folders are a decent solution, and using NFS does indeed speed up performance quite a bit (usually on the order of 20-50x for a file-heavy framework like Drupal!). However, it has it's downsides: it requires extra effort to get running on Windows, requires NFS support inside the VM (not all Vagrant base boxes provide support by default), and is not actually all that fast—in comparison to native filesystem performance.
I was developing a relatively large Drupal site lately, with over 200 modules enabled, meaning there were literally thousands of files and hundreds of directories that Drupal would end up scanning/including on every page request. For some reason, even simple pages like admin forms would take 2+ seconds to load, and digging into the situation with XHProf, I found a likely culprit: