The Constitution states that South Dakota will have two senators. They have two. The fact that one is incapacitated doesn't change that.
It doesn't say just they must have the same number of senators, it says
no State, without its Consent, shall be deprived of its equal Suffrage in the Senate.That's stronger. If a senator is incapacitated, and can not vote, that means that senator's state is being denied equal suffrage in the Senate!