It should be noted that this, by itself, doesn't allow Vecna to identify every spell cast by enemy spell casters.
There are no rules for identifying spellcasting in the Players Handbook -- those rules only exist in Xanathar's Guide to Everything, p.85:
"To [identify a spell], a character can use their reaction to identify a spell as it's being cast, or they can use an action on their turn to identify a spell by its effect after it is cast.
"If the character perceived the casting, the spell's effect, or both, the character can make an Intelligence (Arcana) check with the reaction or action."
Unless there's something else about Vecna's abilities in the adventure module that aren't being shared, the ability to identify spells without an ability check only absolves Vecna from that last sentence; he doesn't have to make an ability check to identify a spell.
Nothing in the text quoted from the adventure means that Vecna doesn't have to perceive the spellcasting, nor does it absolve Vecna from having to spend a reaction to identify the spell. It simply means that once he does so, he does not have to succeed at an ability check. This is explained in Xanathar's Guide this way: "This Intelligence (Arcana) check represents the fact that identifying a spell requires a quick mind and familiarity with the theory and practice of casting."
Because of this, I vote 'Dread Counterspell will NOT work against a spell cast with Subtle Spell."
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Pauper