It's honestly a hard call. On the one hand, I think Kurt, and by extension the audience would've liked to know a bit more about the experiments. Like they just threw the plot line in there and did nothing with it. It could've even contributed to his story in season 4.
But, at the same time, at that point in the series, I don't think that Kurt could've handled it. At that point in the series he still had self-esteem issues surrounding his appearance. Can you imagine what he would've been feeling after hearing that he was experimented on, especially if those experiments contributed to his appearance?
He probably would've been filled with more anger, confusion, and self-loathing than he could bear. Especially since they didn't know the specifics of the experiments, just that they happened. I'm sure they told him at some point offscreen, just at a time where had a little more self esteem. Considering Kurt's intense desire to revive Mystique in season 4, probably sometime before that.