>The USS Fitzgerald is 153m and crewed by 200. It is extremely maneuverable

You aren't kidding...found this video of the same class of destroyer doing a 180 degree turn. Surprisingly nimble. https://www.youtube.com/watch?v=5Vih4tGmqjs

How does that work? Does the autopilot wake someone up if there is an impending collision or are the ship routes fixed?

Nope. Autopilot, like cruise control, relieves you of the burden of driving but not of the responsibility of watch [1]. The Crystal Bay also must have had radar and an alarm should have gone off. Yeah, the Crystal Bay was a drone ship but the Navy is the freaking Navy; moreover they were sailing dark in a crowded sea lane. It's impossible not to fault the crew starting with the captain.

ColRegs Rule 5

  Every vessel shall at all times maintain a proper look-out by sight and hearing as well as by all available means appropriate in the prevailing circumstances and conditions so as to make a full appraisal of the situation and of the risk of collision.

[1] https://www.navcen.uscg.gov/pdf/navrules/navrules.pdf

The crew are not allowed to be asleep. In practice - it happens.

I get that part, but if the whole lot of them went to sleep, they must have been very confident that nothing happens or that they will be awoken before anything happens.

I'm wondering why they would be that confident.

The easiest way to track vessels at sea is using the AIS system[1], which is based on VHF transponders that broadcast position, course, speed, and other useful information. This data is overlaid on the chart by navigation software which also provides configurable alarms. In fact, thanks to AIS you can even track ships online on sites like MarineTraffic[2].

AIS transponders are required on merchant ships above a certain length. Like with all technology, this can make people complacent and rely on it too much. As others mentioned, in this case the destroyer probably switched their AIS transponder off (but should still be able to receive).

Even then, the navy ship would still appear on the radar screen (not to mention its navigation lights), but radar is much more noisy since it can be affected by the environment (e.g. rainy squalls or waves).

The above is based on my experience as a sailor.

[1] https://en.wikipedia.org/wiki/Automatic_identification_syste...

[2] https://www.marinetraffic.com/

There are only one or two people awake on lookout in a civilian ship.

Air-conditioned bridge, slowly rolling waves, practically nothing to see or do... If they're on a typical watch pattern, 0230 means they got out of bed an hour ago and had just settled into the watch routine.

Pretty easy to drift off.

...for 3-12 minutes. Then BNWAS flashes the light, then it sounds an alarm, then it sounds a different alarm both on the bridge and in the captain's cabin, then it sounds an alarm that the entire crew can hear...

However, yes, even if BNWAS were operational the watch could doze off for long enough to miss the fact that they were being passed, but not by enough, by a smaller faster vessel with no lights and AIS turned off.