Formally, yes, Subtle Spell should protect *most* spells from being counterspelled.
To counterspell someone, you need to see them casting the spell; this is not fluff or flavour - if you cannot see the spell being cast, then you cannot counterspell it.
The effects of a spell (A bead of light streaking out of your hand towards a point, a massive wall of ice beginning to encircle you, a sickening green ray, etc.) are NOT the casting of the spell; they are is effect. Casting a spell is specifically tied to its three potential components; Verbal, Somatic and Material. Verbal components are comprised of incantations, words and sounds made; Somatic components are gesticulations and the making of specific motions and shapes with your hands, or whatever else you might use to make the gestures; material components are physical, tangible objects that must be held, manipulated or used in the casting of the spell (the hand used to make somatic components can also hold your material if needed).
Now, if the spell has neither Verbal or Somatic components, or they are negated by subtle spell, then they don't exist and cannot be detected or seen as a spell being cast. That leave Material; in most cases, people replace the material component with a spellcasting focus of some description, and formally speaking there is nothing that requires this focus to give off any particular sign that it is being used as a focus - it does not need to glow, be presented or waved around, or any other obvious thing; the caster simply needs to have it to hand; there need not be any particular signifier at all that gives away a spell being cast.
thanks for your answer.
