There is kind of an ongoing debate about whether the lowers make the ENGINE acutally run hotter, or if the rider's perception of added heat is the thing. Certainly, the lowers block air flow to the rider...that's their purpose. But whether they actually reduce cooling to the engine is debatable, IMO. I have yet to see any hard proof that engine temps rise with lowers installed. Rider comfort? That's a different question.
I leave mine on year round, and I live in Alabama, where it's hot as Hades in the Summer. But everyone's tolerance to heat is different. I've gotten where I just don't like riding when the temps get much over 90 degrees...old age, I guess. Sweat running down my butt crack is not something enjoyable to me any longer.
Windshield height can be changed pretty easily by taking it to a glass shop and having them cut it down some...or just get a different windshield. Heat management can certainly be helped with a proper tune as well.