According to the rules of DND, when a spell is cast, anyone can use the spell counter to try to interrupt the casting of the spell. The premise of successful spell counter-measure is that the counter-measure uses the same spell level as the counter-measure, and the result of throwing d20 dice plus the counter-measure's spell level is greater than or equal to the caster's spell preservation.
Clever modeling will not bypass this rule. Even if the caster uses this feature to cast a spell without making obvious sounds or gestures, if the dice thrown by the spell counter exceed the caster's spell storage, the spell can still be countered.
To sum up, subtle casting cannot ignore magic counter-measures, which is still an effective way to try to interrupt and stop magic casting.