There are three possible versions.
1) following the Tome and Blood rules. Each missing element would increase the spell by +2dc. No movement. +2. no sound +2. No materials +2. Which makes it a dc 15+6+spell level. a dc of 21+ whatever spell level. Not too bad but the realism seems flawed doesn't it.
2) Following what the song and silence stated for disguise spell. A still silent spell cannot be identified. I would argue that if all three were unseen (as example above) you cannot identify the spell until it is already in effect/in place. Other wise, for each missing component it is +2 dc.
3) You are the DM, as such you choose what is right for the feelof your campaign. Is it known in your world's history that spell casters have turned the tide of battle by counterspelling an opponent's spell without any telltale signs. It is afterall your choice.
on a side note, if detect magic were in play, I might allow a spell craft check to identify the school to use a spell from the same school but one level higher to counter it. IE spell being cast is fireball and you use cone of cold to counter. both are evocation spells.