If you are changing ranged weapon types (crossbow to boomerang for exmaple) you would still blink. If you're changing from Shurikens to a stat ammo, I'm not sure. Sorry.
This still causes blinking because Shurikens are Throwing Items and stat ammos are mostly Non-Throwing categorized. It's a pain point for NIN and has never been resolved, short of removing any ammo swap in every single set...which is extremely annoying. The only fix is dressup.