To our knowledge, the Servants may have fought in previous Wars, so that Archer knew Ilya from before doesn't prove anything. Ilya was always a mysterious character, so how Archer knew her could've been explained by several different theories.
Without knowledge of Archer being Shirou, Archer using a variety of weapons doesn't mean that he's creating them. At the time, it seemed like it was simply part of Archer's noble phantasm, him being able to access some shit that stored all his weapon's and he merely had the capability to summon them. And that Shirou uses the same weapon doesn't mean shit. Shirou had been copying weapons he had seen before, like him creating Sabers weapon. He doing so doesn't mean that Saber is Shirou. Mere coincidence.
And going back to Servants having the capability of fighting in different Wars might've explained why Archer has so much knowledge on Shirou's ability. He could've participated in a previous War where there was a Master that used the same type of ability that Shirou is using.
So, to respond to your post, no it's not obvious. Looking back it might seem that way because you know the truth, but without previous knowledge of him being Shirou, there's is no real "obvious" way to say that Archer was Shirou.