Using the same hook more than one times I have several custom modules and each one of them serves different functionalities. Each module contains from few to many hook implementations and inevitably there are cases where I have to use a hook more than one times between the modules, hook_menu for example.
What are the downsides (if any) of using the same hooks more than one times in different modules ? Is that recommended ? What about performance?
Thanks!
That's exactly how it is supposed to work. Hooks are functions defined by Drupal for you to add functionality to the system through your modules. Hooks are like open doors for you to add things.

From Drupal's documentation:


  To extend Drupal, a module need simply implement a hook. When Drupal wishes to allow intervention from modules, it determines which modules implement a hook and calls that hook in all enabled modules that implement it.


Obviously, the more hooks defined in different modules, performance gets hit. But you can't avoid that. You shouldn't stop adding functionality to your modules through hooks because of this.