Surgical removal of the polyps is the treatment of choice. The main reason for this is that the polyps (in most cases), though they can be seen in the ear, they actually originate from the auditory tube. The auditory tube runs from the middle ear to the nasopharynx at the back of the mouth. The polyps can block the airway and cause a sudden onset of difficulty breathing, which if not addressed can potentially be fatal. These nasopharyngeal polyps can also lead to chronic ear problems, chronic nasal problems (sneezing, nasal discharge, infections, loud respiratory noises), difficulty eating (if they press on certain nerves), and Horner's syndrome (the eye droop, 3rd eyelid elevation and small pupil size you referred to in your post).
Generally, the Horner's syndrome that results from the surgery is only temporary. Once the inflammation subsides the cat returns to normal. Of course, as with any procedure, there are no guarantees and it is possible for those things to be permanent. Make sure that the surgeon performing the procedure is very experienced with this type of surgery because there are a lot of important nerves and vessels in this area. Moreover, failure to get all of the tissue means that the polyps will certainly reform. That said, there is always the possibility that additional polyps could develop since it's not well understood how/ why they form in the first place.
I'd recommend you have the surgery done.
Here's a good website for additional information on nasopharyngeal polyps. There is some technical jargon to wade through but it was the most accurate information I could find for you: