When I started NG+, I noticed the Undines from Lake Shisetika were gone...

As they've been more or less the only supplier of the aforementioned material, where can I gather those now? According to Info some other monster drops them too, but as it's not revealed I assume it's in one of NG+ only dungeons?

Are you sure they're gone? They should be at Western Shore (the free map), but they only spawn every 9 turns there. They're definitely there for me. Unless you need them now, you're better off waiting and doing Suina's second set of quests (with Lenia Nui/Lacus Lenia), there are far more available at Central Lake.

Oh, they are now. I guess I had to do quest 28, and related events in town first. Revisits before that didn't yield any Undines, or even the portal where they spawn from, in Western Shore...

Yes, some enemies in free maps only appear after you beat certain missions. You can also get it from cards in chapter 3.