But has it ever been adjudicated? Lots of things "have precedence", but that doesn't mean they are Constitutional. There is clear conflict on this within the document, and a fiat declaration that a comatose or permanently disabled Senator that cannot ever hope to fulfill his duties is NOT a defacto vacancy is not for you or me to decide.
Someone with standing has to file suit. Maybe an official of the State of S.D.
I'd love to see them win, and then some States pass laws on what constitutes a "vacant" Senator. Romney to Kerry:"You've missed 87% of the Senate votes while running for President. I'm declaring your post vacant and appointing a successor, unless you stay there and work."
It is unlikely that there would be a successful suit in this matter since the Supreme Court has no power over Congressional rules wrt Congress's membership and/or rules.
Separation of Powers pretty much rules out any such suit.
Since these matters are explicitly given over in the Constitution to Congress my bet is no court would declare Congressional actions regarding membership to be "unconstitutional".