I think they set them out as bait? For the kaiju. If you think about it, fancy boats wouldn't be the kind to take out to see to attack them. You'd want something much tougher.

[Raidou really hadn't had time to think about all this, what with the whirlwind that is his life here, but now he wishes he had.]

I believe it stands to reason they have at least a little bit of foreknowledge regarding the rifts and attacks.