nope, the Super Dragon Balls can pretty much grant anything. The Namekian Dragon Balls were both bigger and more powerful than the Earth Dragon Balls. The super Dragon balls are planet-sized. Were comparing this to Dragon Balls that fit into the palm of your hand or basket ball sized.
Their creator is one of the top gods that are second only to Zeno himself, so.....yeah, functionally omnipotent. If Zeno can destroy 12 universes, its perfectly possible for the Super Dragon Balls to bring them back. If they are still there.
and no, Whis has shown at times to PREVENT the end of the world. He doesn't make a show of it, but it seems the Angels purpose are to moderate the Gods of Destruction as well as assist them, to keep them from going too out of control. Especially given that he is given a staff to rewind time if Beerus destroys something he is not supposed to.
It could be that restoring the universe like this, could be the Super Dragon Balls actual original purpose given the destructive nature of Zeno himself. He is innocent to the cruelty he inflicts upon people with his destruction, but no universe = boredom for him. So I'm thinking he ordered there to be way to restore things so that he may endlessly have fun with the universe as his plaything, endlessly destroying and restoring things in a vast cycle. It would explain the very childish password required for the Super Dragon Balls, since Zeno IS a child.
Of course, I also theorize that the Gods of Destruction are originally there to moderate ZENO's destruction. That originally, Zeno dealt with everything personally and therefore constantly destroyed universes in his displeasure while one of his attendants restored things to keep reality from being destroyed entirely. So the Gods of destruction were eventually formed so that the power could be delegated and things that displease Zeno would be destroyed on a smaller scale before he could ever see them and thus he would have more time for fun. Of course then things like the Guardians were formed so that these things would be dealt with on an even smaller scale so that the Gods of Destruction weren't required for everything.
Thus it explains the entire structure of divinity: the entire purpose of the gods is to limit and contain anything that might displease Zeno on multiple levels from Guardians at the most subtle and weak, to the Gods of Destruction. While the super Dragon Balls were kept around in case anything serious enough happened to merit their use.
Edit: I mean, there are still the Gods of Creation and its canon that there has to be a BALANCE of Destruction and Creation. Zeno destroying almost everything won't be a balance. Else, why bother creating this entire divine bureaucracy in the first place?