I have not noticed any negative effects. It has only been a year, but the 3m tape I used has been great. I did not notice a sound difference but to be honest the top is down on mine 95% of the time I am driving it, the AC / heat is off and the fabspeed is on full blast
In all seriousness though from the little bit i did use the blower before i did it I noticed no difference. But it was one of the first repairs I did (3 months or so after buying) so take my opinion with that reference point.