I ride a Rabeneick TS5 2017 Alfine 8, bought in 2018, with about 5000km on it (mostly commuting on asphalt, in all weather (mostly dry), some easy forest trails). It has BR-M395 hydraulic disk brakes with resin pads, with BL-M395 levers and SM-RT54-S 160mm rotors, vertical dropouts, a bolt-on-axle hub dynamo (probably DH-3D37-NT) in the front, Alfine 8 IGH in the back. I frequently experience disk rubbing (both rhythmic and continuous) on both wheels. I usually managed to fix it by re-centering/adjusting the brakes and/or bending the rotors by hand, but after braking hard the noise often returns.
It got continuously more complicated to adjust, until a while ago I was unable to make the front brake silent, so I brought the bike to a LBS, who installed new pads. It was fine at first, but after a ride the noise returned. Being fed up (and also because the LBSes here are ridiculously expensive), I bought new rotors and the tools to install them. It took ages to adjust the wheel, brake, and rotor to make them run silently.
Today I got a flat and had to take off the front wheel to take out the tube and submerge it in water to find the whole. Patching it and putting it all back together was easy enough, but the brake was (of course) misaligned again and I again had to fiddle forever to adjust it properly.
So the questions are - do all (hydraulic) disk brakes need that much care? Is just this model particularly bad and more expensive ones are more reliable? Do I need to replace the brake itself (rather complicated because of the hydraulics)? Should I just ignore the noise? Am I doing something wrong? Should disk brakes only be used with thru-axles as the wheel position is fixed? Just as an example, the Surly Troll "expedition touring" bike has vertical dropouts and disk brakes too. If you get a flat in the middle of nowhere and had to take a wheel off to patch/replace the tube, how would you re-adjust the brake? Sounds like a nightmare!