The Shedinja will have the same EVs as your Ninjask when your Nincada first evolves. If you want your Shedinja and Ninjask to have the same EVs you can just Effort Train your Nincada before you evolve it. If you want the two of them to have different EVs then you will want to wait until after you evolve your Nincada to do any Effort Training. Of course, in Emerald, you can use the EV reducing berries if you need to.
So, in short, if your Nincada had 100 Attack EVs when it evolved, then both Ninjask and Shedinja will have 100 Attack EVs.
