Yes. When you download Pokémon Bank and Poké Transporter, you will need to remove the restrictions on systems in the Nintendo 3DS family for Shopping Services within the Parental Controls.
After you complete the download, you will also need to remove the restrictions on using the internet browser each time the software will be used.
For a detailed guide to System Settings, please refer to the following article: http://en-americas-support.nintendo.com/app/answers/detail/a_id/10530.
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