Don't know if it has effects on sleep, though anecdotally I sleep very well. However before using f.lux I experienced headaches from time to time after long days in front of various screens. It wasn't a regular occurrence but I'm pretty sure it was related to those long hours.

Since I started using f.lux all day (not just at night) several years ago those headaches have a been a thing of the past - it basically doesn't happen anymore.

I know f.lux is intended to be used in dark environments but since I rarely do color-sensitive work and prefer the lush, warmer color temperature (3800K for me), I see no reason to change my all-day use.