I have one main domain hosted on cPanel shared server. Under the Main domain I have hosted 3 addon domains. My Hosting Provider has set 100 emails to send per hour.

Now my concern is should I send 100 emails through individual domain or total I can send 100 emails including main domain and addon domains ?

Who is your hosting provider? When it comes to send bulk email through a shared plan, most of the time it is better to use a dedicated email blast service such as vertical response or constant contact. The reason is that they are better equipped to handle the volume. Thus you dont have to schedule mail to go on scheduled intervals of x amount.