There are plenty of champs with weird AP ratios. Poppy on her anti-dash zone, Jinx on her chompers, Ashe on her ult, Sion on both his shield and his roar, etc., etc.
I asked this question and a Red answered: "Abilities without scaling at all are very, very rare, so when we have an ability that should not scale with items, we put a scaling with a stat that the champ doesn't want to build, but it essentially means 'no scaling'."
I question the relevance of useless scalings instead of no scaling at all, but Shen is definitely not alone in this case, and shouldn't be treated as a special case...