NOT stupid questions, and I think it’s a logical suggestion. I’m actually surprised the vet said he needs to be under anesthesia to clear the ducts, since it’s pretty common I used to use a tube of cream that would clear and dry up a weepy eye, but maybe this is much more severe.
First, by all means ask your vet if it’s possible. Bunnies are at risk under anesthesia like the rest of us, and yes, things can go wrong, so there is a risk. But it doesn’t sound like it would be an unusual risk, so see if your vet is comfortable with that.
I also think you could get a second opinion for your own comfort and the sake of your bunny’s best options. Is your vet an “Exotics” vet? They specialize in small animals (rather than dogs and cats), and birds, so they are more experienced with rabbits. If your vet is more general, see if you can locate a vet near you that mentions specializing in exotics. Then get him looked at. It’s an extra expense, but you may be more comfortable with the new vet, or reassured that your current vet is doing well. Either way, you will have more direct info. regarding your bunny’s health and what to do next.