It loses majorly to a Dialga G Deafen-Lock as well as any deck with a Vileplume in it. And since a lot of decks are running Vileplume nowadays to counter the threat of SPs, Shuppet Donk has fallen out of favor.
In actuality, Shuppet Donk stopped being used when Spiritomb came out, because any deck that used Spiritomb ended up using several, and the Spiritomb user could do a lot more harm with its hit-and-run Pokemon (Gengar AR, Magnezone SF) than the Shuppet person could do.
In summation, Shuppet Donk, due to trainer-lock decks, cannot set up as efficiently anymore. That is why it is not often used.