The reason is WB writes accessfiles and phisical subdirectories for all created pages.
If you do not use some directory above the root and you would create a page like admin/framework/include/temp/templates etc that could casue problems.
Especially when a page like that is removed, the complete directory structure would be removed.
Creating a page like "config" in the root would overwrite your config.php and completely disable the website including the admin.
As long as you are sure you will never create those pages you can remove the pages directory. If you create websites for 3rd parties (customers) it presents a very high risk the customers breaks the website without knowing.
a more safe solution is to use something like
http://short.allwww.nl although it still has some issues with special modules/pagetypes.