If they told me that they had it and it would be waiting when I arrived? Yes.
If they told me to wait until they sent me a notice that it would be available for pickup? No.
Now, that said, I am of the opinion that Apple needs a better in-store system for pickup of website items. If they had that, it wouldn't be such a hassle sometimes to pick up purchased items. An "express line" for pickups, as it were. Hell, even Best Buy has one of those.
But, with the way it is set up now, your disappointment is solely on you because Apple told you to wait until they let you know it was ready.