For some reason I am thinking that you are talking about the chrome wind deflectors that mount to the front forks, under the faring, or the ones that mount to the lower part of the faring - not faring lowers that mount to the crash bars.
If I am right, you should be able to run either one year round without any problems. If they are the faring mount and are adjustable, just open them in the summer.
True faring lowers are a judgement call - seems to be a 50/50 split to leave them on or not. I've had mine on since 1999 and have never had engine problems.