First of all, like has been said multiple times, remember that this is Emet-Selch's perspective of it all: people who know NieR Reincarnation better than us have confirmed that's how the storytelling is normally, and it checks out pretty much one-to-one with Emet's framing and use of language ('malformed' is wording that he, and only he, uses when referring to sundered people). It's not actually providing new information, it's just dressing up and compressing the story he's told us.
It's hard to read anything much into the language part; it could be an objective truth and making sort of a Tower of Babel story... or it could just be, as pointed out before, Emet looking at everyone screaming in wordless pain and confuusion and going 'welp, I guess they can't talk anymore'. You're not wrong that them losing that language would arguably see them abandon that continuity of civilization (again, Tower of Babel), but remember that the fact the rest of the Scions can understand the Ancients is an actual scene beat.
What might be worth remembering, though, is just how the Ancients recorded information. We know from Akadaemia that they weren't above written notes, but most recording and communication we see actually seems to be through various forms of crystal--seen in the Watcher's tower, as well as Anamnesis Anyder. But not only are both of those mediums fairly susceptible to damage, even the WoL and the Scions have to exert some effort to read information in crystals. It's entirely possible that even if you do understand the language, it's just not worth the effort to read.
...especially since you have to consider the possibility that they might not even care. When we came to the Anyders, we were paying attention because we knew people motivated by Amaurot were fairly pressing concerns to us. But the recently sundered? They don't have that context, and might have more pressing concerns like 'finding food' and 'avoiding the giant walking landshark'.