[@Yukitamas]

If the shot is headed toward the thickest part of your armor, and you are confidant that it will be deflected, then yes you can hurt yourself more by trying to move out of the way, and instead having the arrow hit a more lightly armored area. 

Also keep in mind that Hercules skin does not work the same way as Armor and Babr-e Bayan does. If an A rank attack hits Hercules, then he gets hit with an A rank attack, and his invulnerability basically does not exist. Babr-e Bayan and Armor heavily subtract from the power of an attack even if they are penetrated. 

If Hercules sees an NP arrow being charged up and thinks that it's in the A rank range, it makes sense for him to try and deflect it. Rostam seeing an arrow that was not charged up, or released via name or anything, had no reason to suspect it was anything more than an especially fast glittery arrow, which would do minimal damage to him even if it was an A or A+ ranked attack.   

Yes, Agility does cover a wide variety of things like dexterity, finesse and raw speed, all of which contribute to being able to dodge or deflect arrows, hence why it's harder for Rostam with his C rank vs Hercules with his A rank. When you have less of any one of these things it covers, dealing with fast moving objects becomes harder for you.