I'm not a smoker, so I can't speak to that issue, but I have suffered from GERD and was non-responsive to 40mg Protonix twice a day. The answer to your question is yes...you can have "Silent GERD" in which you get the damaging acid in your esophagus and don't know it. That's not what I had, but lots of people here have had it.
The GERD I experienced wasn't as severe as some have described on this forum (including yours, from the sound of it). It was severe enough, however, to cause my asthma to be untreatable. I was on high doses of inhaled steroids, and periodic oral steroids to keep me breathing. I was using a nebulizer daily to keep my lungs open. My steroid dosage was enough to cause adrenal insufficiency symptoms, and thinning, bruising, and tearing skin.
Finally, in February, I decided I had to take the chance and have the Nissen Fundoplication surgery (laproscopic). I wish now that I'd done it long ago. My lungs are clear for the first time in years. I had been coughing tons of phlegm out of them all the time. (Coincidentally, I actually had a "smoker's cough" even though I never smoked!)
You definitely should find a good GI doc locally, and work on finding out what's up. You need someone you can communicate with, and who will really listen to you. If you need to shop around, by all means, do that. If you decide to opt for the surgery, be sure to select your surgeon VERY carefully. It's the most important part of that decision. The negative posts you see on the internet are mainly from people who had an unqualified, inexperienced surgeon do the job.
If you search with the Google window at the top of this page, you can locate posts and strands that might answer some of your questions.
Good luck, Maggi!
Be sure to keep posting and asking questions. There are a lot of members here who have been through what you're going through, and I'm sure they'll have helpful comments for you. It's vacation time, so some of the regular members are coming and going, but stay around and I'm sure you 'll find lots of support here.