The rules here are certainly not clear, because they generally assume that the act of casting a spell has some noticeable element. Notice I did not say component, because I think the rules are silent on parts of spellcasting that are codified components versus those that occur without any sort of codification, such as the wiggle of a finger, change in breathing and other flavor bits that happen when a spellcaster makes the magic happen, as it were.
Back to the topic at hand, since the rules are silent here, I think it is well within the GMs purview to impose a penalty to the Spellcraft check to identify a spell without components (V, S, M). Since there is no real increase for spells with just one, I would guess that this penalty is not very large, perhaps only as much as -4.
This is, of course, up to your GM to adjudicate.
Jason Bulmahn
Lead Designer
Paizo Publishing
Edit: I should also note that I also agree with James, that a strict reading of the rules says you can make the check, without penalty, regardless of the spell's components.
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