Do you meet specific problems with virtual directories?
1) this is not a YES or NO question. It really depends on your need. If you need many, why not create many?
2) virtual directory count is not a well known cause for performance issues, (or we can say it doesn't have an impact on performance.) Besides, never experience any other virtual directory originated issues about performance.
3) remove a virtual directory can stop all access to it. But not sure if that's what you ask for.
Please note that virtual directory and application are two different things, check if you actually need to know about application instead of virtual directory.
http://learn.iis.net/page.aspx/150/understanding-sites-apps-and-vdirs-in-iis-7/
Regards,