There are several reasons to empower your council. In rough order of importance:
First, the council has to be empowered to enforce realm peace. If you want to change your succession laws, none of your vassals can be fighting one another, and without realm peace that might not ever happen.
Second, empowering the council opens up one or two advisor slots if you're a kingdom or empire, respectively. That gives you someplace to put those powerful but incompetent vassals who want council seats.
Third, if the council isn't empowered, there will be constant faction plots to empower it.
Fourth, the more the council is empowered, the higher your vassal limit.
What I normally do is let council power rise until I have my succession law where I want it and am ready to enact Imperial Administration (instituting Imperial Administration requires that you have absolute rule i.e., that the council not be empowered) and then un-empower them. At that point you should be powerful enough that factions aren't that big of a deal and Imperial Administration gives you a big boost to vassal limit; there's really no reason to let it become empowered again except role-play, or if you are really, really big and really need a higher vassal limit.