Cant help but think they need to revamp this site a bit to keep interest of people. For example I find it annoying how messages are gotten to from notifications instead of a message box. Makes it REALLY annoying when you have more than 1 message. Also if multiple people like your group post you get messages for all those likes instead of just how many people liked it? Same with comments... software developers here be slacking!
You can get directly to your messages by clicking on the envelope icon, bypassing the alert (it should clear the alert as well). So I don't understand your annoyance with this.
As for comment/reply alerts, they don't all happen at once. I think it's a safe assumption that most people would want to be alerted to comments/replies as soon as they happen. However, you can adjust this in your alert settings, by disabling the web alerts, enabling the email alerts, and setting the email frequency.
I'm not sure if the email frequency effects the web alerts. Maybe a web alert for a web accessible digest would be possible? @Admin?