Now you're just being silly, Rkhet. For one thing, the shadows would drastically reduce the Encounter Level, as shown in the DMG, because circumstances would make the battle much easier for the PCs, just like ambushing a bunch of sleeping, unarmored idiots with cotton stuck in their ears would make the battle tremendously easier. It reduces the challenge, thus reducing the Encounter Level, thus reducing the percentage of normal XP and treasure that the DMG recommends awarding, exactly as per the DMG's guidelines. So while the Shadows wouldn't take XP away like cohorts would, their assistance in the battle would, circumstantially, reduce the Encounter Level and thus cause the PCs to earn less XP/treasure than normal.
Secondly, as the original poster described, his player found out about this stuff but there is no in-game reason/way for the character to have learned this knowledge too. So if the player uses that knowledge without having his character learn it in-game, through interacting with sages who know this stuff or finding the lore in a library (or through an appropriate Knowledge-Religion or Knowledge-Undead check), then the player would be metagaming and, thus, cheating. I'm sure that Shadows aren't such common monsters that average folks in-game would know about their abilities, let alone the specifics. It'd be a pretty high Knowledge check DC to learn about how shadows control the victims they make spawn out of, or it'd require talking to a sage that is knowledgeable about the subject (generally meaning either an undead-lore expert, or just any ol' sage who succeeds at the right Knowledge check).
And, in-game, the character has no reason to go looking for this knowledge specifically; he might take up an interest in incorporeal undead maybe, and figure that it might be useful to control such minions, but it would take a while of research and such come across the fact that Shadows could be so useful in combination with a Shapechange spell. Additionally, the character himself would not even know the capabilities of a Shapechange spell unless he made a high-DC Knowledge (Arcana) check or learned about it from a sage who made that check or is just very familiar with high-level magic. And there likely aren't a lot of folks in the game-world who can cast 9th-level spells, or who are simply familiar with the specifics of such spell effects. Let alone willing to share such knowledge with a dubious fellow. Thus, also, few people around who have any way (or any reason) to produce 9th-level spell scrolls and sell them. In-game, it just isn't so simple as "I read the monster manual and player's handbook, so I'm going to do this and this, because I say so and I don't care if it's impossible for my character to know this stuff already." At least, not in any game that maintains a semblence of roleplaying and continuity.
Lastly, the DM has the right to change stuff around that normally isn't supposed to be character-knowledge or player-used, like monster stats, and the DM has the right to use monsters and such from books the players haven't read yet. PCs aren't supposed to know everything (or much at all) from the Monster Manual, even, and so long as the DM is consistent and fair, there's nothing wrong with modifying the monsters and not telling the players about such changes before they encounter the beasts. Through Knowledge checks or visits to sages and libraries, the players could learn about such monsters and whatnot, but they cannot be assumed to just know all this stuff automatically. The only houserules players need to be made aware of beforehand are those that directly pertain to playing their characters, not DMing. It's not rude or mean. No moreso than having newbies encounter a stirge, for example, when they're unfamiliar with it; you're not obligated to explain the critter's abilities for them beforehand, just because they're new and haven't read the Monster Manual or played D&D before. They'll figure out how to beat it and move on, and you're not being a spiteful DM just because you let them figure it out themselves in-game, through encountering a few of the little buggers.