This is expected.  A null value makes it look like the preference does 
not exist to the UI code, so it doesn't bother to run the hook.

I found what was happening. If the pref value is null the hook will 
not be called, example:

$_prefs['add_source']['value'] = null;
$_prefs['add_source']['hook'] = true;

I don't know if this is an expected behaviour but changing the value 
to an empty string fixed my problem.

That is exactly what I tried but only works for horde prefs. I tried 
with your master branch, any idea why this could be happening?

Works fine here.  Example prefs.local.php:

<?php
$_prefs['add_source']['hook'] = true;

I was trying to use prefs_init hook for "add_source" and 
"search_source" prefs but the prefs_init hook never runs (I already 
have 'hook'=>true on those prefs)

I am doing the same for horde preferences without any problem.

PS: I tried to use #horde channel to confirm this bug but I got no response.