I'm largely reading novels or technical text as epubs on e-ink devices and the only time I've ever had issues like those you mention is when publishers have included "arty" css. I wouldn't tend to read magazines in that format, probably pdf on a tablet or desktop if I needed to.

For some of these things - like ragged right and kerning - I think you have to almost train yourself to notice them, I've been reading a long time and can't recall ever being bothered by either.