That's why Bleach characters' endurance is crazy compared to that. They can survive building-busting explosions with few scratches. Although Ishida has slightly weaker durability than "normal". But I am fairly sure he could protect himself against a BP Direct hit even if he wouldn't take it very kindly.
Also we can't forget Ishida's crazy speed and rate of fire. He would dodge and intercept almost any attacks of Archer. I think Archer's chances to win:
In textbook stats: 20%
In actual combat: Roughly 55% or a bit less.