If I understand you correct, you don't want to convert your database, but want NodeBB to work with users, that still will be in your existing database (MS-SQL).
It's possible, by creating your own database driver for NodeBB.
But, actually, it's not so easy. If you don't have high skill in programming, it's near to impossible.
has anyone run NodeBB using a custom SQL user database like this?
Maybe, but I never heard about it. You could try to wait for the NodeBB core developers. They, probably, know something, that may helps you.
But perhaps I should add a not in the sign up agreement that "by signing up you agree to receive emails from us" or something like that, to be safe.
If you're in the EU, this wouldn't constitute as opt-in. The EU states that a user must specifically click a button that states "I want to receive these emails". Unless it's regarding their account. So, if the daily digest included notifications, it would be fine, but if it was just new topics, I'm not so sure. It should be fine either way, as you've said.