Comments on articles to notify who exactly? The article author? You can of course bypass the notification trigger for all notifications since CB Activity notifications themselves are just using triggers too.

Ok, so the trigger does work and it is the grouping logic that's preventing it from sending further emails. I suspect it's only sending the email the first time someone comments. So User A comments and email sends. User A comments again and email does not send. The reason it's doing this is because there's nothing to store. As far as the notification logic is concerned they've already been notified about that users comment. Is that what's happening?

If that's the case then you might need to just send the email earlier. Instead of waiting for the notification to store in CB Activity just fire off the email immediately. You can do this by simply changing the trigger.

FROM: activity_onAfterNotificationEntityStore
TO: activity_onBeforeNotificationEntityStore

The before trigger is fired before any of the notification store processing is done so it should trigger every single time a comment notification is made. You risk this being pretty spammy though.

Sorry, I meant to say.

FROM: activity_onAfterNotificationEntityStore
TO: activity_onBeforeNotificationEntityStore

Give activity_onBeforeNotificationEntityStore a try. That would at least ignore all the grouping logic.