I wanna use tweaking to get Darkrai and Shaymin, but I'm worried it will harm my DS
Generally, no. Glitches and hacks can cause damage to the save file on game, but not usually the system.
Pokegen, Pokedit, and other, less safe hacking devices will not harm your DS.
Some(very few) hacks can harm your DS, but they're major hacks, like a fake game card.