Blocking a notification doesn't affect performance, though if that app might ever wish to notify you of something important you wouldn't get the notification.
Bear in mind that some system apps are genuinely important, some are just crap that the manufacturer added (or were paid to add), but you will get the same warnings about interfering with them regardless. So the trick is really to know what the app does and make your own judgement, but knowing what it does is the important bit.