They removed silences from mobile assassins (Talon, Kassadin, Leblanc) since it prevented you from retaliating before they either retreated or instantly killed you. They haven't touch sliences on immobile champions such as Cho'gath, Malzahar, Soraka, and Fiddlesticks because silences are not an issue; silences on specific champions can be, but not the CC in general.
Morgana's Black Shield isn't an exception, it's an ability. It it's purpose is to block CC and provide a magic damage shield. The way you phrased it, every ability in the game is an exception since no two abilities function in exactly the same way.
As for your example with rengar, Rengar's passive jump doesn't have cast time. Neither is his jump completely oppressive, it is more the fact that he can now dump the double "Q" onto your face. If Rengar is flying towards you, you can stun him or knock him back to deny his jump or deny the damage that he pumps into you after the jump. Lo- and beyold, counter play.
You somehow completely missed the point of that example, which was that you wouldn't make a single exception (silence disabling Rengar's passive) to a general rule (passives are not affected by silence). That example had absolutely nothing to do with Rengar's balance or counterplay.