if almost all

Not at all

Sequencing is neither reference based or de novo. It's how you analyse the data afterwards.

Even for well characterized genomes such as humans we can discover new things using de novo assembly, such as complex structural variation.

The point is there is structural variation in genome between organism from the same species , so you can speak about De novo sequencing for every organism to my point of view ! If you check all genome reference organism have N , so genomes are partially sequenced because of the limits of assembly like low complexity region for example.