Which host is that small shop on and is it already on 11.2 or still 11.1? Because I tested exactly this on staging for the coffee shop last night, after your post made me nervous about our own setup.
Short version: the Bcc is gone for that one. On 11.2 the saved Cc/Bcc values are still in the database and still show in the settings, but for three emails they are ignored, new account, reset password and the confirm email address one. I made a test account. The owner's Bcc on new account mail did not arrive. The order emails with the same Bcc arrived fine.
So nothing broke silently on the order side. Only the account mails.
And I'm pretty sure this is on purpose not a bug because those three carry a login link or a reset link and a copy of a reset link sitting in the bookkeeper's inbox is a key to the customer's account, which is a weird thing to hand out on purpose.
You can get it back! The recipient filters for those emails still work so a dev can add the bookkeeper their in a snippet.
I'd not do it for the reset mail though. For new account I'd think about it, for reset I wouldn't.