Oh yes! We were at the beach for the past two weeks and the car was sitting outside the whole time in the sun (what sun there was, out of 14 days only 4 were sunny) and I noticed it was worse than usual. It actually can be startling at times, and always seems like its coming from the passenger side of the dash. I can only equate it to a house settling. My best guess is that its some part of the structure or interior of the car settling after its been sitting. It doesn't happen except for in the first 10-15 minutes of driving. Its garaged at home, but I noticed the cracking was louder while it was sitting outside at the beach.
I guess its normal, I've never had a car do that before though, even a previous LS400 nor the 04 LS430 my dad drives now. The wood veneers for instance in the ES are real I suppose it could be them expanding and contracting (the air conditioning rapidly changing the temperature of the interior and the internals of the dash as the air circulates through the system) with temp, but again my dad's LS430 doesn't do that and it has as much if not more wood than the ES. After about 15 minutes of driving and once the interior reaches a comfortable temp it stops.
Its definately strange. See what your dealer says, I've never brought it up with mine but I will at the next service stop.