Officially it's for "engineering works" (even though it's a brand new line).
In reality the vastly reduced passenger traffic on weekends in that far east end of London means they can save money by just not having any trains, train drivers and station staff working. Also, weekend journeys on public transport in London cost less for passengers, so TFL (transport for London) make a lot less money. It's a pure cost cutting measure.

It's not just the Elizabeth line...on almost all weekends anywhere from 25% to 40% of the London transport netwrork is not running due to "engineering works"....which is total BS. I know of no other major city worldwide that shuts almost half it's metro network down every weekend just because they make less money.

Don't get caught out.