Drupal 6 - Grouping Modules together
Grouping modules is allowed in Drupal, when the modules are not already modules. Because, the modules are registered in System table by the location of the module. So, Changing the folder structure will result in fatal errors.

If you would like to change the folder structure then you need to disable the modules and uninstall them. After that, you can re-enable them after changing the folder structure by grouping them.

Note: Make sure you won't lose any data when you un-install the custom modules. Take a backup of database and source code before doing any changes for safe side.