Let me speak from my personal experience towing my Sidekick...4x4, manual trans, auto hubs...
As was stated earlier, placing the trans case in N locks the outputs together, so the front driveshaft, diff, half shafts will also turn. From my experience, this really isn't a huge problem, IF your cv boots are in good condition. I had a torn boot on the driver's side half shaft...I made it about 150 miles and got flagged down because it looked like the Kick was on fire....smoke rolling off the front left wheel. I got out to investigate and there is black grease slung all down the side of the rig, and the left outer CV joint was completely toasted. As in, all my years of wrenching, I have never seen a CV joint that looked like this thing! Through messing with that I figured out the driveshafts were locked together, so placed the case in 2 Hi, pulled the rear driveshaft loose and tied it up underneath and continued my trip. On the way home I left the shaft attached and just left the case in 2HI. My conclusion is that the front locking hubs have nothing to do with that problem. Leaving the transfer case in 2HI actually leaves you with fewer parts moving, so as such, less heat, less friction, etc. Seems to me this would be much preferred to pulling with it in N. Now ideal situation? Twin stick shifter on the case you so you select N on both sticks and in theory transmit no movement into the transmission.