Do you realize how hard it is to get rid of these games? Most of them are busted, barely work and aren't even indicative of what is shown in the preview pictures. There are MORE of these than there are fan games. These games are trash, some fan games aren't. Point is, Nintendo of America would have to hire an ENTIRE team to track, find and remove these games on a 24/7 GLOBAL scale. It's highly unrealistic and these fakes have proven themselves to unaffect sales anyways.

There are several reasons
1. The pirates directly accessed nintendo's servers prior to launch. While the copyright infringement is a larger overall problem, the piracy was more upfront and thrown directly into nintendo's lap.
2. It is easier to stop the pirates. Nintendo has direct electronic access and control of your account, and the pirates directly contracted with nintendo giving them the power to cut the account through the user agreements.

The copyright fuckers have to be found (ie- their actual address and identities, which might require nintendo to first serve the people hosting the games), served with a cease and desist, and then sued and forced to go through a civil trial. A trial that might be extra hard since it might be an international law issue since these copy cats might be in china or something (so it might be hard to get jurisdiction.. at all).

Shutting down the copy cats is a long and involved process that costs money. Pirates can be taken down with a few keystrokes.