Why did the Boeing Max operated by Lion Air disintegrate upon crashing in the sea from a low altitude?
Because of a high speed impact

The official accident report published by the Komite Nasional Keselamatan Transportasi (KNKT) shows the data from the FDR (flight data recorder) for the accident flight. This is the altitude and airspeed it recorded:



As you can see, the aircraft reached an airspeed of around 450 kt before the FDR stopped recording (the Vmo of the 737 MAX is 340 kt according to b737.org). The altitude was around 6000 ft, which I would not really call "low altitude". Also note how fast the altitude dropped towards the end: the aircraft went from about 5000 ft to impact in only around 22 seconds resulting in descent rates in excess of 10,000 ft/min.

The report further says:


  The recovered wreckage identified consisted of, but was not limited to, parts from
  the left and right engines, both main landing gears, parts of the empennage, parts of
  the forward and aft left passenger doors, parts of the wings, a flight crew oxygen
  bottle, and parts of a circuit breaker panel. The damage to the aircraft suggested a
  high energy impact.


So the primary reason for the disintegration was the high speed at the time of the impact. No commercial airliner could possibly survive this. Have a look at this car crash test at only 200 km/h:


(HIGHSPEED CRASH TEST - 200 KM/H Ford Focus vs. Concrete Block on YouTube)

The car is completely destroyed by the impact on a concrete block. As Zeiss Ikon pointed out in the comments, "at even 100 kt, water is harder than concrete". And 450 kt is over 800 km/h, meaning 4 times faster (i.e. $ 4^2 = 16 $ times higher kinetic energy). Nothing that can still fly could possibly be built to survive this.