Why do high-level players flick through control groups constantly?

Most pro players do it to "warm up" their fingers early in the game. That way, when they need to produce tons of meaningful actions in the mid-to-late game, they are "limber".

Whether or not that helps or is the best method for warming up, however, is questionable. Tzenes, our resident SC2 guru, addressed this in an answer to an earlier question on improving your APM:

Epinephrine has some interesting effects on the human body, one of which is to contract the blood vessels in your fingers right before a tournament reducing circulation and making them feel 'cold.' Spamming keys is less effective at over coming this than taking a second and flexing your fingers.

A lot of amateur players will spam actions to get a higher "APM" number. As has been said countless times, though, it's not how many actions you have per minute but what you do with your actions that is the difference between victory and defeat.

You are not missing something important (all your points about checking to see if something is done is correct), players are simply keeping their fingers warm so that when it comes time to fight, they are ready to react quickly.

Day[9] does a good explanation of how tapping through control groups helps your overall game play in these two videos:

http://day9tv.blip.tv/file/4742049/

http://day9tv.blip.tv/file/4772601/

As you continue playing, these slower repetitive motions becomes quicker and quicker which to the rest of us seems insanely fast.