Thanks for the reply, @Osiris and @JuergenAuer.
I read the docs carefully once again, and I guess that I missed understanding the difference between Virtual Host and Domains.
Let me list them all.
Virtual Host 1
Virtual Host 1 is the home of the domain name example1.com
example1.com has total five domains
Virtual Host 2
Virtual Host 2 is the home of the domain name example2.com
example2.com has a total of 105 domains
Virtual Host 3
Virtual Host 3 is the home of the domain name example3.com
example1.com has a total of two domains
Virtual Host 500
Virtual Host 500 is the home of the domain name example500.com
example500.com has a total of two domains
In this set-up, the Virtual Host 1 is within the 100 Names per Certificate limit. However, Virtual Host 2 exceeds that limit. From Virtual Host 3 to Virtual Host 500, there are just two domains each, and thus there is no any limit issues.
However, the total number of accounts (Virtual Host) hosted on the same dedicated server exceeded 100 and reached 500. But I don’t need to worry about the number of Virtual Hosts; I only need to look into the number of domains in a Virtual Host.
Is this the right thought?