Here is a guide created by a pro player for Shen on top lane runes, masteries, and items.
3x Movement Speed Quints: I like to move fast to harass enemies in lane and one of the biggest things with these is once you teleport in onto an allie you're going to want to taunt someone most likely or chase down someone who's low. What better way to do that then to have increased movement speed! They're perfect for initiating and escaping too!
3x Flat AP Quints: Personally I prefer the MS quints for overall game utility but if you really want to dominate the lane then having this early will surely help you do that. The added bit of sustain and DPS makes him that much stronger in lane.
It's really up to you on what quints you like using. Both are viable.