A DM ruling is the only answer we have
As far as the official rules go, no one knows; they never said.
Here is literally everything the game has to offer on the subject of how material components actually work:
Components
A spell’s components are what you must do or possess to cast it. The Components entry in a spell description includes abbreviations that tell you what type of components it has. Specifics for material, focus, and XP components are given at the end of the descriptive text. Usually you don’t worry about components, but when you can’t use a component for some reason or when a material or focus component is expensive, then the components are important.
[…]
Material (M): A material component is one or more physical substances or objects that are annihilated by the spell energies in the casting process. Unless a cost is given for a material component, the cost is negligible. Don’t bother to keep track of material components with negligible cost. Assume you have all you need as long as you have your spell component pouch.
[…]
XP Cost (XP): […] The XP are treated just like a material component—expended when you cast the spell, whether or not the casting succeeds.
(Player’s Handbook, pg. 174)
(I just love that “just like a material component” in the XP entry that introduces a new fact not otherwise established about material components.)
You could argue that attempting to cast the spell without the right component means the spell fails, and then argue that—per the line in the XP component section—the insufficient material component is still “expended” even though the casting failed.
But there are a lot of problems with that analysis. For one, “to cast it,” you must have the material components. Without them, you can’t cast it—not “it fails,” but “you don’t cast it at all.” How that works narratively isn’t described at all, but it’s tough to say you cast it—and it just failed—when one of the few rules we have is that you can’t cast it. For what it’s worth, the “Rules of the Game: Magical Oddities (Part Three)” article by Skip Williams (an author of the 3.5e PHB) doesn’t list lacking material components as one of the things that can cause a spell to fail. Furthermore, even if you did rule that the spell fails, it failed because of the lack of an onyx of sufficient value—the onyx of insufficient value wasn’t a (valid) material component for the spell. It’s not at all clear that it would be “annihilated” when it isn’t actually a material component at all.
@Peter Cordes points out, though, that you could argue that you do cast animate dead—it just isn’t powerful enough to target what you want, and having no valid targets, fails for that reason. That’s a plausible rationale for losing both the spell slot and the onyx.
But we can’t really definitively come down on one side or the other. The FAQ doesn’t talk about material components at all. The Rules of the Game articles do, but don’t address this question (I checked). Rules Compendium just repeats the stuff from the Player’s Handbook.
So the DM must make a ruling. The authors apparently never conceived of this as a concern, or just assumed that a spellcaster, knowing how their own spells work, would simply always know what material components they need. For me, I’d just say nothing happens—not even a lost spell slot—since you don’t have everything you need to even try to cast a spell. Peter Cordes has a pretty good argument for ruling the opposite way. Either of those might be consistent with the rules we’ve got. But then, “consistent with the rules we’ve got” when those rules clearly don’t contemplate this situation isn’t worth much, so a DM ruling is really the only way to go.
