1st off, they would never flood Fontaine so that we wouldn't be able to explore it as is in the future. 2nd there are almost as many chests in Fontaine(311) as Inazuma(357) and Fontaine's map is only half done. To say there are not many chests here is premature to say the least.
I'm pretty sure he wasn't talking about Fontaine as a whole. He was talking about blowing up the fortress and making that specific area inaccessible. And the fortress does have very few chests, hence that comment.
I wanted to side with wriothesely so badly, I had zero sympathy for lyney and didn't mind if diver boy bit the dust, dang it genshin, let me speak my actual thoughts.
Yeh there has always been amazing lore in this game (Dragonspine, Enkanomiya, Narzissenkreuz, King Deshret, Khaenri'ah) and now it's finally time for it to feature more heavily in Archon Quests