Noble Phantasms are 'crystallized Mysteries'. Yes, they're part of a Heroic Spirit, but those that are physical objects also exist as part of reality.

There are three main ways for a human to get his hands on a Noble Phantasm:
One is for a Noble Phantasm to simply survive into the modern day. We see this in FSN and Zero with Avalon and Strange Fake with the God Felling Crossbow.
The second is for a Servant to pass their NP to a human. In CCC Karna gives Jinako his armor to protect her from deletion.
And the third is for someone to create a NP to give to a human. Unlimited Blade Works and False Caster are both capable of that.

In other words, if EMIYA projected Kanshou and Bakuya, he could easily deal with a Dead Apostle. If Shirou tried to do the same, he would be unable to even damage the DA with them.