Well, to Counterspell, the mage in question has to declare that they are doing so (SR4A, p. 185). It's a free action to turn the counterspelling "on/off", so all they have to do is to make the declaration. No matter how many people are protected by the mage doing the Counterspelling, they only make one roll of the dice--most likely as soon as they declare they are they are Counterspelling.
The way I'd rule it is that as soon as they turn it "on", they roll the dice to generate the hits, which are then applied to all resistance tests until the mage turns it "off". If they turn it back "on", they'd get a new dice roll--but I'd say that turning it "off" would take another Free Action (same as Change Linked Device Mode), so they'd only be able to turn it "on" or "off" once per Initiative Pass.
The second roll is totally in secret, made when the NPC casts the spell on the mage.
Of course, if you have a group that is good with separation of character/player knowledge, you don't really have to worry about "secret checks", since you can simply point out that the player knows something was cast at their defending mage, but the character has no idea on a failed Perception check.