I'm gathering by his screen name that he has a 1999 Prelude, and all 5th gen. (1997-2001) Preludes have the immobilizer.

When they cut the key, they probably used one of his originals to use as the guide to cut it with. If you go back to the parts shop of any Honda dealer, right next to the key cutter is the computer to program the new keys. All they do is sit both keys in the computer after they cut them, press a button, and in about 10 seconds the new key is programed. So, they most likely did in fact program it, only since it didn't take any time to do so, he didn't think they did.