From a technical side of things, what happens to the chapters that are taken down? Are they instantly gone and deleted forever, or can they be preserved somewhere, just not visible to the public? (for legal reasons it is a hypothetical question)
Nothing was truly lost forever as everything on MangaDex is constantly polled and harvested by dozens of popular illegal manga rehost sites. They rip official translations from official sources but also steal fan translations only posted on MangaDex. Then they add a ton of ads to the site, and it's an easy way to make money if you're hosting in a country that won't comply with international law. To certain sites, DMCA notices are funny emails they laugh at.
So yeah, I generally hate supporting those sites in any way (and will run adblock if I visit them), but it's unlikely any content was truly "lost" forever, since it was already being ripped off so much.
That said, I don't think this is the end of MD or anything. For one, MD mainly covers manga, manhua, and manhwa. This DMCA only culls a slice of influential manga. As far as I know, nothing from Korea, China, or Southeast Asia was touched.
It would be very ironic if the site called "MangaDex" served every type of content -except- manga, but the site would still have plenty of purpose. Japan isn't the only country with interesting stories in the East, not by a long shot.