Currently hooks are in ~/includes/hooks/ and global.
There is even module dependent support with ~/modules/MY_MODULE/hooks.php .
Could we please have a look at getting theme support as well.
Think of all the benefits you have for example with the 'functions.php' file system in Wordpress.
At the moment it is just another file that is not contained in one place, making updates and upgrades more complicated than needed.
What about if we want to change between themes and a hook should only apply to one specific theme.
Making child themes work is a big step in the right direction to start.
Now we just need more integrated support.
Having something like ~/templates/MY_CHILD_THEME/includes/hooks/ would be great , or just even ~/templates/MY_CHILD_THEME/hooks.php would be great.