Even still, all those throwing sprites prove is that at some point, they intended on using them. Now, whether it's a hidden item we haven't found (Seth!) or they just scrapped the idea, that's the question.
I wouldn't look to much into this.In a platformer such as this the main character is usually the first thing that's coded after the level, so my guess is they coded Megaman before they made the final decision on the weapons.
Is this part of the mystery of Megaman 9, It's been a while i never heard a new update on Megaman 9 :[