This is a big part of why I dislike consolidating downloading and viewing.
I've been using PerfectViewer on a tablet for viewing for ages. I'm sure there's a better one and would be game for recommendations, but I am very used to this app and its quirks.
There exist any number of ways to download and sync the chapters to my device. I currently mostly use the mangadex-dl script and a syncthings folder and it's no trouble. And all my read chapters I can just move into an archive drive where I'll have them if anything ever happens.
This is standard practice with media. You use something like MPV for viewing and the downloading is handled elsewhere.
I mean, the answer to that is clearly they should structure their service to store the absolute least possible personal information needed to allow the service to function so that when a legitimate law enforcement agency comes knocking they can honestly say they don't have much.
Which... appears to be pretty much what they do.
I agree with you. Losing the protection of a right -- even one as fundamental as privacy -- is by definition not a violation so long as that happens through due process. Now we can certainly talk a lot about what level of process is due, and I'm sure it will be basically unanimous that current standards around the world are FAR too accommodating to law enforcement, but at least in principle a warrant justifies the invasion of privacy. That's what the warrant is for.
This story kind of makes me want to switch all my stuff to ProtonMail.