There are a lot of unknowns with Warforged, because Cannith didn't actually build them up from the ground up, but rather used designs of the Creation Forges and Creation Patterns they cribbed from the ruins in Xen'drik. Cannith doesn't understand the entirety of Giant Magic, mostly because it's Epic Level stuff the giants themselves learned from the Dragons, but they instead found that they could bypass understanding it with the Mark of Making; which is why you have to have a Mark of Making to operate a Creation Forge. Or you can be Epic level, learn Giant Magic, and work them legitimately. It would be a first in millenia, but this is DnD we're talking about, we all know we want those epic storylines.
The point is that no one really knows how exactly Warforged get their intelligence, their souls, or even the ability to taste and smell (which really has no practical purpose). There are plenty of black boxes in Warforged, and Cannith was just beginning to test the true limits of Warforged creation when Cyre went kasploot. Cannith lost a lot of resources and leaders in Cyre (unlike Phiarlan, which was also based in Cyre, but all their leaders were conviniently away when things went pear-shaped), and by the time they began to pick up the pieces, the Treaty of Thronehold swooped in banning the creation of Warforged and ordering the dismantling of the Creation Forges. If you want more answers about why Warforged are the way they are, you'll be best off asking Baron Merrix d'Cannith. But then, he might think you know about the Creation Forge he illegally operates, and send his construct assasins after you...
And I respectfully disagree that Warforged don't make good infiltrators. Can ordinary infiltrators stay submerged underwater for any length of time without special equipment? Can they survive without any food or water, or stealing some? Do ordinary infiltrators need to sleep? Infiltrators are meant to be unseen and unnoticed... and for those times when you can't avoid being seen, Warforged were purchased by every nation to supplement their forces. Just kill one, hide the corpse, impersonate it/him/her with magic or mundane disguises, and be on your way.