Strange problem. Have a 2003 4Runner sport 85K miles. Now wife's car. Since I bought it new have had a weathertech sunroof deflector on it.
Only sunroof problems was about 10 years ago and dealer replaced track or something for 1200.00 out of warranty but called main office and they split the cost with me.
Dont think anything to do with the problem. But sunroof may get opened once every 5 years.

Which is 3 months ago I decided to remove the deflector and liked the look better. Threw the old one away.
I dont drive it much. Later noticed I now get a lot of wind noise from the sunroof. Tried cleaning and silicone on all weatherstripping.
My guess was all those years the 2 small clamps deformed the weatherstripping. But cant actually see anything by just looking.
Any ideas. May just have to order another deflector. Never had a wind noise problem before.

Thanks

 

I think you may have answered your own question.