Yeah, weapons are only for normal attacks.

If you want the character to have a weapon while "casting" (which is what the animation is considered to be) that'll have to be set up in one of the character's Battle Charset PNG files.

Just copy the "Right Hand" animation to a blank area (if you did it like the RTP there will be space on the second file - if not, just make another). It may take a while to line up.

After you DO get it to line up, copy a weapon from the Weapon PNG file you want to use, and paste that over top of the new animation you set up. You'll have a new animation that you can use for that casting animation!

(WARNING. It's obvious that there is a major problem with this: The weapon will always be the same, no matter what weapon you have equipped. The only way to counter this is by making an animation and corresponding skill for EACH WEAPON and having a parallel process Common Event check what you have equipped. The parallel process should then equip the proper variants of the skills.)

I'm not sure why Enterbrain decided that RPG Maker 2000 / 2003's skills should all be considered "Magic", instead of simply skills. But at least a workaround exists, even if it is a pain to do.