Very normal for a lot of airlines/people to do this. Altouhgh I've never seen people turn off their nav lights.
Ever fly in fog with the strobes and LL (landing lights) on? With the reflections, the strobes can actually be redirected into the flight deck which can temporarly freak the pilot as he/she's reading his/her instruments during a seriouse time, the LLs can also create glare problems. This also may bother other aircrafts in the vincinty as it is hard anyways to figure out what directions the light is coming from and may confuse them. I've seen pilots perform CAT2 approaches (I know we're talking about 3's..) and even the strobes from them light up the entire airport with the fog and you can't tell what direction it's comings from...
Again this is usually with strobes and LL's, I'd never turn off the Nav's, turning off your nav would mean your aircraft would be invisible every couple of split seconds as the beacon only flashes every split second and usually nav's are not as bright as strobes or landing lights.
