As I understood the problem, there was/is a maximum number of missions generated for the bulletin board (I believe it's 20 missions). A permit-locked mission is therefore "stealing" a mission slot that would otherwise be available. Systems surrounding permit-locked systems would be difficult to find missions for - which, for some permit-locks, are the very same factions you need to gain rep with in order to gain the mission.
Take Alpha Centauri as an example. Being so close to Sol, most of the missions there would "naturally" have Sol as a destination. Without a Sol permit, that means it'd be virtually impossible to find a completable mission in Alpha Centauri, as most of them would be permit-locked.
Or take Procyon, for which Sirius would be a "natural" mission destination. You want to rep up with Sirius so you can get the Sirius permit? Well, too bad, because you can't; all the Sirius Corp missions in Procyon are asking you to go to Sirius to complete them.
I do not know if it is still the case, but I do know that there were some exceptions to the "no missions to permit-locked systems" rule. Over a year ago I was working down near Cemiess (in Imperial core space), and one of the systems down near there had been Expanded into by one of the Achenar-based factions. That Achenar-based faction would offer you missions to go to Achenar. I already had the rank for the Achenar permit, so I don't know what would've happened if I didn't.
Personally, I think the Superpower capitals (Sol, Achenar, Alioth) should be a special mission generator; there should always be a small chance that any superpower-aligned faction will want to offer a mission to travel to the capital. Likewise, missions from the capital out to the various colonies should be abundant.