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Because they make perfect sense on a bike designed to be used for travelling distance/touring etc.
A brake cable is far easier to find in some backwood town than the correct type of hydraulic fluid and a bleed kit...and personally i'd rather change a brake cable in the middle of nowhere than bleed brakes.
As for flat bars, why wouldn't they? Not everybody wants their bars to be higher thanks to riser bars...not everybody wants drops...so flat's are ideal in those circumstances.

I guess here was meant: why mechanical disc brakes on a bike with flat bars, THUS NOT WITH DROP BARS.
With drop bars there is almost no option for hydraulic disc brakes. Not that disc brakes are a good option there, but that's a different story...
But I agree. Mechanical disc brakes (almost all of them) are rubbish. There are enough affordable, well functioning, maintenance free hydraulic disc brakes for flat or riser bars.