How to make it?
Making a clafoutis with pits one day, and without pits the next, doesn't really allow you to compare: you'll have more of a memory of the first when you make the second, than of its true taste.
The simplest "method" I've found is to make 2 (small) clafoutis with the same recipe, putting pitted cherries in one and pitted cherries in the other, and tasting one then the other, for immediate comparison.
The 2 clafoutis
In 2 small molds, I placed the same quantity of whole cherries (300 gr) in one, and pitted cherries in the other.
In the 2 molds, I poured the same amount of clafoutis batter (250 gr).
And then off to the oven to bake.
How did it turn out?
We tasted them, lukewarm, and with several people, to try and get different opinions.


The result is that, objectively speaking, the difference in taste between clafoutis with and without pits is not at all marked.
However, we did notice that, in the case of pitted cherries, there's a small, very interesting acidity, which is present in the heart of the whole cherries, and not in the pitted ones.
In fact, I'm afraid we're a little influenced by the color and appearance of the clafoutis: you can see the one with pits, and when you taste it, you think you'll find a difference, which is (in my opinion) a little overrated.
But, as always with taste, there's no arguing with it, and you'll probably have to repeat the experience to make up your own mind.
If you're really looking for that "cherry-stone taste", I'd recommend pouring 1 or 2 tablespoons of Kirsch into the clafoutis batter.
In summary: For cherry clafoutis, leaving or removing the pits during cooking changes the taste very little, if at all.