Amsterdam to Lake Como

You can fly very cheaply in under two hours.

Nope. Overnight and fast are words that do not go together when talking about trains. Most night trains cover a distance in 11 hours that a day train covers in 7 hours, like the Thello from Paris to Milan. Add on the Thalys from Amsterdam to Paris in 3 1/2 hours, a station change in Paris, and a final 1 hour regional train to the lake. It is one long 18 hours.

Flying Amsterdam to Milan looks like a good alternative.

Public transport is easy and direct from either Milan's Malpensa airport (by Malpensa Express train) or Linate airport (by Starfly or ATM brand shuttles) to Milano Central train station, where you can catch trains to various parts of Lake Como. Check both airports at www.skyscanner.com.