Yes.
The thing that really brought this to my attention was a close high-school friend of mine who, in high school, was "one of the dumb kids"... that is, not learning-disabled, but not on the honors/college-bound track. When we graduated he was reluctant to come visit me in college, because I'd gone to MIT and "he wouldn't have anything in common with all those smart kids." Etc.
The thing was, it was clear to me that he was every bit as smart as I was, and in fact when he did come visit he was astonished to discover that he fit in with my college friends quite well... he'd thought I was some kind of fluke. He's since gone on to a successful career as an industry analyst. Every once in a while I tease him about being "one of the dumb kids" and he acknowledges that no, he was just wrong about that.
I wish I understood better how the transition happened, because I suspect that a lot of equally capable people don't manage that transition... and, as you say, drop the habit.
One of the big variations I see between people is the amount of energy they habitually put into thinking, and I haven't seen this discussed anywhere.
General advice about improving health and lowering intellectual friction would seem to help increase the ability to think, and ideas like "take five minutes to consider the problem" adds impetus, but I'm not sure what the general difference is between me and most people, or Yvain and me.
Intellectual drive isn't an unalloyed good-- cranks have high drive combined with low self-editinig, and some types of depression include a compulsion to think about topics that cause misery and/or inertia. Part (all?) of the value of meditation is getting some time off from thinking. Still, increasing intellectual drive would probably be a good thing for a lot of people.
Has anyone found that rationality training or anything else increases the default desire to think?