So yeah, Link now has the ability to fire projectiles going sideways.
Apparently, ZC doesn't seem to like certain animated projectiles such as arrows and magic, and perhaps rocks; Now, I did have the H- and V-Flip options set, but it seems that it didn't affect anything.
Right. Weapons weren't designed to support animation, since they expect their horizontal tile to immediately follow their vertical tile.
Better support for customizing weapons would be a good feature, but will need to wait for post-2.50.
Why not set up a Horizontal/Vertical Firing Sprite for items like the Arrow in the Action tab of the Item Editor? It'd probably be the best way to make this work...
Ask again after 2.50.