The LEDs are usually whiter and can affect the bet result of the filtered light. The red, amber and blue lights aren't affected, but green light tend to look bluer than usual. I've noticed many airfield lights and indeed traffic lights where the white light behind the lens has been changed. And I've noticed some aircraft have rather blue looking green lights as well.
It probably doesn't make much difference, but interestingly, the International Maritime Organisation (the maritime equivalent of ICAO) in the Collisions Regulations (COLREGS) does specify chromatic parameters for light colours and if you change the bulb in the starboard nav light, you must also change the lens. And where I sail (Hong Kong) the local Marine Department have stopped people for having the wrong colour green light!
They should be using coloured LED rather than coloured lenses. May not be the case though. The colours are specified by ICAO (and I think the FAA).
WRT boats, mine has LED nav lights, and they use a clear lens.
I have noticed a strobe effect from different sources of LEDs (others don't seem to notice this) including from newer cars and some street and home lighting. I assume that the LED react to 50 Hz RMS very quickly in a way that incandescent lights don't. Would this also apply to an array of runway lights?
The problem with feeding AC to LED's is they switch on and off. It does not affect an incandescent bulb, because as the voltage passes through 0, the filament remains heated.
The LED should be fed DC, and I would assume that this would be the case with runway lights.