http://webzoom.freewebs.com/xmuppetsb/ZC%20Content/Test%20Quests/25rc3test.qst
In this quest file, I have stumbled upon two problems with scripted weapons. The 'Gohma (Laser)' enemy in particular uses a scripted weapon (lasers). Here are the problems:
1) This weapon still hurts Link while he's invincible
2) Rings and Peril Rings do not reduce damage taken from this weapon.
Scripted weapons
The relevant script isn't included in the file, so I can't check it, but I would guess that it's setting Link->HP rather than using built-in damage handling.
That's because I import the .z files for ghosted enemies to save room in the script file itself.
The relevant scripts can be found here: http://www.purezc.com/forums/index.php?showtopic=51270