I own the Armada book, no need for the online PDF.
First off, it says that you must purchase a fleet commander in the 13th Crusade list if you have any capital ships, not a point restriction (that's the incursion list). Second, any number of capital ships may be upgraded to a deamonship.
So as written, these list's don't contradict any written rules.
And I can see a fleet of Daemonships working excellently! Your only used to one or two daemonships on the field at a time, not a fleet. Could you imagine the chaos (no pun intended) of the enemy when every one of these ships in placed on the table at the same time right in the midst of the enemy fleet!?! In the pure Slaanesh fleet, the enemy would have a really hard time doing ANYTHING because most of his fleet would be under the -3 Ld (I would imagine). In the other, replacing the Carnage with the Desolator, is harder to play but still has good advantages (re-roll for the Styx being one of them).
-Zhukov