It's not explicitly clear in the description of the Spellwarp Sniper, so it would have to be ruled on by the DM. That said, the clue that would decide how I would rule were I the DM is that Sudden Raystrike isn't limited to "magic" bonuses:
If you get a sneak attack or sudden strike bonus from another source (such as rogue or ninja levels), the bonuses on damage stack whenever both abilities would apply to the same target. (Sudden Raystrike ability, Complete Scoundrel, p. 64)
This implies that the essence of the ability lies in directing the ray to a critical location based on skill at aiming and a knowledge of enemy anatomy/weaknesses, not on some magical something-something that modifies the magic of the spell.
Hence, were I to rule on this as the DM, I would say that Sudden Raystrike applies to any ray that requires the caster to make an attack roll (indicating that it's under their control), including those from scrolls and wands.
(I would make it hinge on the attack roll only to eliminate unusual cases where a magic item casts a spell that is usually a ray but doesn't require an attack roll, such as a hypothetical figurine that can emit a ray of frost that "unerringly" strikes the nearest fire elemental within 30 feet, for example. The ray of such an item wouldn't be under the Spellwarp Sniper's direct guidance, and so I wouldn't allow Sudden Raystrike to apply.)