Supercard DsTwo has better firmware compatibility and doesn't require a console exploit, so as long as you keep the card updated, it is okay. Just make sure you dont update your 3ds until you update the supercard.
For me if you want to emulate the DS the best option is on Android, use DraStic and a controller that holds your phone... it's clunky but it works insanely well. The next best option in my opinion is using a New 3DS XL, not really emulation but hacked it works really well.
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