G-good god. ;_;
You know, I think everyone had a feeling all along that Yuuko wasn't supposed to be there. The shop was cut off from everything, and you could only enter the shop if you needed to. It explains a lot, and I'm not surprised to heart that Yuuko was already dead.
Watanuki's rather emotional outburst was completely justified. With meeting Yuuko, his life changed, and all for the better. One can only imagine how he must be feeling, having his mentor, and the closest thing he has to a parent disappear.