I asked Nintendo support if my Pokemon would be safe after doing a system transfer, and received this response:

"Thanks for writing. You will be pleased to know that your Pokémon will be safe during a system transfer, all you need to do to access them on your replacement Nintendo 3DS system is purchase a new subscription to Pokémon Bank."

Do I really need a new subscription to Pokemon Bank after a system transfer? Will my previous one no longer work?

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    I highly doubt it, once you do a successful system transfer your NNID will be tied to the new console, so you will be able to access your old Pokebank account.
    – pinckerman
    Jan 14 '17 at 3:59

Unless your one year subscription is up, I don't think you'll have to repurchase. That sort of thing is tied to your NNID system combo. While I have not done this transfer myself I have found at least one example elsewhere where a person confirmed that their pokebank still worked. (source)

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