According to Grimoire Nier, the replicants aren't always in the same exact roles - they mention Yonah being either Nier's daughter or sister in the two versions as an example. Because reproduction is wholly decoupled from the actual Replicants themselves, overseers have greater control over who to introduce into the environment; as well as when and where they'll do so. The medieval level of technology and society also assists in keeping records from generations back vague - in addition, the system was never designed to cope with the Replicants actually being sentient beings instead of docile shells. Much of what we see may be the result of frantic improvisation on the part of the android overseers, with different communities around the world coming to different arrangements.
As for what Popola and Devola did, their catastrophic sympathy with Nier and his group is one part - with Nier being erased from memory and the twins dead, it would only become easier to place more of the blame directly on them, even extending to parts of the disaster that weren't conscious decisions on their part. With the way things were at the end of the first game, they may have even seen reason to believe that what happened was their intent.
Anime loves some Axis iconography. The suicide mission of a Pearl Harbor descent was no coincidence.
