Drupal developers will always have their own style of coding, and module file structure conventions. On a project where there are two or more developers, it can be beneficial to have a unified way of structuring your custom modules.
One of the reasons why I prefer structuring custom modules is because it makes it easier to find functions or block of codes when debugging.
When all the team members’ are using the same file structure, it is easier for each of them to jump in and help each other debug things if needed.
If there are people on your team who don’t code the same way no worries. Simply having the same filename conventions, and placing functions in different files, in the same manner, makes your project more organized and easier to maintain in the long run.
Here's an example of a file structure that I have used on one of my projects:
module_name
-cck_content_types(exported content types, if necessary)
-js
-css
-images
-includes
-templates
--blocks
--views(overridden views template files)
--others