Yes, it will determine if the Seed Soldier is prone or not when it hatches. Note that the Cadmus can't deploy prone if it uses AD:4 due to the rules for Aerial Deployment.
Yes... (though not AD, obviously) Pros: You will have a prone camo marker which will be indistinguishable from other prone camo markers (i.e. they won't know if it's a seed embryo, a shrouded, a caliban, or a downgraded malignos). Cons: When you (auto)hatch, you remain prone and cannot use the change in silhouette that would normally happen to then attack something with surprise shot in that order from behind cover. Edit: Ninja'd!