What does repeating beeps mean during charging?
No, its not notifications beeping. 
I have a dropped iPhone 4S here, that has a cracked screen. 
Plugging it into a charger results in a constant beeping every 6 seconds exactly with no display. I have no idea if it's because the display/touchscreen is damaged or if the phone has crashed and is displaying a blank screen as i have no idea of the extent of the damage. 
I'd say it's related to a serious hardware failure that the beeping occurs. 
It's not a notification issue as the phone doesn't have time to boot up iOS before the beeping starts. Beeps way too soon and notifications wouldn't roll in regular as 6 seconds exactly for over an hour.