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You don't understand how annoying the noise was! And if it was the hub, surely a sign that it was on its way out.
Bike shop agreed it's the brake rubbing though so should be an easy fix thankfully
lemonade-
I've ridden 800km with an improperly seated tyre. Annoying at slow speed, dangerous at high speed. I'm very well versed in what annoying is. Anyway, as I said of my hub, it was making noise, I kept riding it, it stopped making noise. I'm still using that hub maybe 5 years later.
As for brake noise, well I rode a QR bike across Europe with disc brakes... I've had my fair share of squeaks.You should've been able to diag that by spinning the wheel and either eyeballing the disc in the pads to check for contact or squeezing the pads slightly when the noise happens - it will change the noise, so you know it's the brakes. I'll often pick up grit in the pads and then to get rid, very quickly stab the brakes to dislodge or move it. If it's constant then you can recentre the pads or bend the rotor or to fix it.
hippy
I mean, if the dynamo hub still works, it's just making a noise, I'd keep using it. Might try some spray lube to see if that helps but there's no way I'd build a new wheel just because of some noise.