I would follow your instincts and combine. You might as well extract the super, the bees have an overstocked nest already. If you set the nuc on top of the old brood nest, the bees are going to move a lot of honey up if there is somewhere to put it above the new queen. If it is not fed sugar and medications, that is not a bad thing. Just make sure they have a super to take it or you will have another swarm.
If the deeps are not contaminated with fed sugar or medications, it would serve you well extracting at least one of them if they are plugged with honey. You might extract anyway and save it for feed.
If the deeps are not contaminated with fed sugar or medications, it would serve you well extracting at least one of them if they are plugged with honey. You might extract anyway and save it for feed.