If Nintendo does not shut down these projects their ability to protect their products in the event of real theft vanishes.
At face value it appears as though Nintendo is simply inept when they don't act until after these projects (Pokemon Uranium/Another Metroid 2 Remake) are released
.
However, I believe that they are willfully allowing these projects to complete and release before issuing legal threats with full knowledge that they will never really remove them from circulation.