Whoa are they that different from a typical motorcycle brake? Because I never had a problem with those, all the way from 1990s japanese scooters. They are simple, reliable and don't require much maintenance. They even work ok on 75% water-dot mix on completely weared-out pads if you can't fix'em on the road. Worst thing that can happen is hose rupture, which is extremely rare, good hoses just work forever, brakes becoming a bit mushy after about 10-15 years, which you adapt to.
I think hydraulics are overkill for bicycles, but apart from that what's the problem?
They can be very very fiddly.
They get contaminated fluid - presumably from shit cylinder seals. They can be difficult to tune (too much travel, not enough). They can be fiddly to change pads. The pistons stop working on one side (binding up), they can leak, etc.
Combine all that with an electronic, wireless gear shifter that’s in close proximity and the roadside repair in the rain can be miserable.
Don’t get me wrong, I like them a lot but most my shop visits are for brake repairs. I have to work on them every few weeks as I go though pads in as little as 6 weeks.
I've never worked on a motorcycle, but I have worked on hydraulic brakes on several cars, including when I was recently given the opportunity to learn how to bend and flare rigid brake lines.
The problem on bicycles is that everything is small and light, and that nothing is really standardized at this point. You need a bleed kit for mineral oil, and a different one for DOT fluid. Each of those probably comes with a few different adapters for the various threadings. Barbs, olives, and flare nuts aren't standardized across manufacturers either. There are three or four different ways to just put a caliper on a fork or frame. There are a further three or four ways to put a rotor on a hub. That means you're stocking more hubs and pre-built wheels as well as rotors. There are easily a dozen common brake pads, probably many more if you start looking at the obscure stuff.
At the handlebars, the drop-bar brake and shift levers are super tightly packaged and integrated. At the high end of the market, you might be able to get rebuild parts, though I never had to do that. Otherwise you're replacing a pretty expensive component, assuming it's even available. The market is still moving pretty fast as we've gone from two-by to one-by drivelines.
Cheaper non-integrated flat-bar brake levers are relatively benign to replace if you have to, but you still have to chop and reterminate the hose and bleed them. On the flip side, you can probably forget about getting rebuild parts.
Compared to a car, and I assume a motorcycle, the tolerances on everything are tighter. The room for gaskets and O-rings is smaller so leaks develop more easily and water contaminates the fluid more easily. The size of the fluid reservoir is vastly smaller so there's less reserve if you have a small leak. You're moving less fluid overall, so the margin between mushy and useless is pretty small.
We've come from a world where you needed two types of cable (road and MTB), one type of housing, and generously a half-dozen kinds of pads for cable actuated rim brakes to this. It's all doable, but the amount of stuff and tools you have to have on hand in a bike shop has goddamn exploded.