A vacancy is not created by illness of a Senator only by actual death or resignation. Thus, the "equal sufferage" clause does not come into play. Effective representation does not apply either. There is precedent for long terms of absence by ill Senators.
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."