I use GoToMeeting daily, and I see the same two pop-ups in every single meeting.
One is the "You are muted; click here to start the meeting unmuted". The other happens when you are muted and make a sound; it reminds you that you are muted and gives you the option not to remind you again.
After using this software for 2 years, they are just annoying noise. I'm fully aware that I start meetings muted and when my microphone is muted, and I don't need the constant reminders. Starting the meeting muted is an explicit choice in the preferences, so it shouldn't trigger a reminder.