oh great, now that i know archer is shirou im gonna have to rewatch all the episodes to pick up on any subtle clue...

in eps 14 archer called ilyasviel "ilya", which surprised her. thats probably a subtle clue.
archer knew that hercules had multiple lives even though, i think, no one told him about his hougu.
i realized that both shirou and archer have the same eyebrows.

i think the biggest reason why people couldnt match archer with shirou is the fact that they have different hair colors. even their eyebrows are different colors, which could mean one of two things. either his hair color changed by magic, or, in the future, shirou dyes both his hair and eyebrows, which would be weird.
im also surprised that archer didnt try to get it on with saber. shirou finally gets a second chance to see her but he doesnt do anything....

I am the bone of my sword.
Steel is my body, and fire is my blood.
I have created over a thousand blades.
Unknown to death nor known to life.
My power can break a mountain, and my sword can part a river.
Have withstood pain to create many weapons.
Yet those hands will never hold anything.
So as I pray, Unlimited Bladeworks.

i wonder, do those phrases have any special meaning?