After doing some more digging, it turns out that roughly 20% of NFIP policies are subsidized, and the up-to $30b debt was authorized by Congress in 2012 due to the shortfalls.

80% of the policies (the non-subsidized ones) are thought to be actuarially sound, barring unintended consequences of out-of-date flood maps.

So, I'm not terribly surprised. Were it operating like a traditional insurer, it might even be doing fine (especially if it had some other reforms such as eliminating or having better oversight over WYO policies).