You can definitely only notice the rationality lessons if you already know them explicitly. I wonder how great the effect is when you're playing the game but don't know about the lessons. My guess: not very great. People can figure it out by instinct. It makes them use the hypothesis-testing skills they already have, not improve them. Most of the difficulty (for me at least) is not in the hypothesis testing, but in multitasking enough to find out what multiple balls do at once, then tracking them all as they bounce around the screen until you can tag them all.

Also, it's a short game, one you're unlikely to spend enough time doing for it to mold you. If you really want to get good at hypothesis testing, I recommend taking up programming. Debugging often stretches my hypothesis testing skills like nothing else I can think of.