I am currently designing an encounter with an animated ship carrying a massive cargo of animated objects. However, the entire thing loses its magic when all that a player needs to do in order to realize that it's animated is a D13 Knowledge Arcana check, plus things like detect magic of course. After a previous inquiry stated that animated objects could not be crafted from magical material or could use wands, I am baffled as to how to naturally increase the stealthiness of the ship and its cargo. So how can I hide that it's all animated?
Animated objects created with Craft Construct (rather than by casting the animate objects spell) do not inherently have any magical aura. They are not temporary magical effects (as with the spell), they are actual creatures with the Construct type. Construct-type creatures do not inherently have a magical aura, despite being magically-created, and animated objects have no special rule to this effect. Note this line from antimagic field:
The spell has no effect on [...] constructs that are imbued with magic during their creation process and are thereafter self-supporting (unless they have been summoned, in which case they are treated like any other summoned creatures).
Using Craft Construct to create proper animated objects means you get “constructs that are imbued with their magic during their creation process and are thereafter self-supporting,” which means that there is no magic to detect with detect magic or suppress with antimagic field.
Moreover, the DC 13 Knowledge (arcana) check to recognize information about animated objects listed on PFSRD is specifically marked Fan Content – the actual rules specify a DC 10 + creature’s CR check to know “abilities and weaknesses,” which for animated objects varies from 10 (CR ½) to 21 (CR 11). However, either way, these are the checks necessary to know things about animated objects – not the checks to recognize that a given object is animated.
Instead, the animated objects would be making Stealth checks, or maybe Disguise checks, against Perception. The situation likely justifies you giving them a considerable Circumstance bonus to their Stealth, too.
Knowledge Arcana represents knowledge of existing magical things. If the animated ship is something newly created, or has sailed from so far away no one has even heard there was land there (much less what it is called, who lives there, etc.), Knowledge Arcana wouldn't supply any information about it.
For Knowledge Arcana to deflate your encounter, you'd have to let it do so. When the players roll, just tell them they've never heard of such a thing.