I would not book anything online ... I don't believe their system is reliable, especially outside of Mexico. If you're worried about a cabin ... arrive in La Paz a day or two early and go book ticket and cabin a couple days ahead of departure.
Only time I've ever seen Ferries full was during a big Football tournament vs. Mazatlan and during Easter holiday. And even then, it was just for one or two crossings where things were jammed up.
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