A digital superinteligence (should I expect it to be organic?) will be either very concentrated or backed-up everywhere. On the first case traditional explosives will give us better bang for our bucks, and lead to less collateral losses. On the second case, nuclear weapons would destroy us much sooner than the AI.

On the case of aliens, the entire problem is how to reach them. If we can get some weapon into them, yes, a nuke would probably be marginally more effective than a lump of lead, but not by a large difference.