Can we add SSL certificate to an add-on domain? is a common question and is answered in http://forums.cpanel.net/f5/can-we-add-ssl-certificate-add-domain-124977... and other pages. A summary of answers is presented here for people planning multiple Web sites with SSL certificates using the Drupal multisite feature or the Domain module.
You know that Drupal can accept several domains pointing to one Web site and Drupal can sort the access out based on the requested domain. Multisite then directs the request to a unique settings.php/database combination while the Domain module uses one unique settings.php/database combination then sorts out the Web site data when accessing content. SSL certificates act earlier and this creates problems.
The basic SSL certificate covers one domain and is loaded when your Web server is working with the IP address of the Web site, not the domain name. You can load only one SSL certificate for the request and the certificate can handle only one domain. If you want to create three Web sites with SSL certificates, create separate Web sites with different IP addresses.
There are simple multiple domain SSL certificates and they handle what we usually call subdomains. One certificate can handle www.example.com, forum.example.com, and git.example.com.
There are many brands of certificates out there with some wild claims about what some of the certificates can do. Some of those certificates do not work in some browsers or have reduced function in some browsers. It would be good to list the results of using those certificates here.
One option is to use multiple port addresses. Domain www.example.com could point to forum.example.com:80 and domain forum.example.com could point to forum.example.com:8080. You can then use a different certificate per port. Many common low cost Web hosting accounts do not let you change port numbers making this a non option, an unchoice, (insert other Monty Python style terms here).
Now, back at your planning stage, what do you do? If you are using SSL certificates, you are probably selling something online and will make some money. If you are using a cheap hosting account then you can afford to put each Web site on a separate hosting account with a unique IP address and a simple SSL certificate.
You can easily move a multisite site to a new account because the database and files are separate. Hmmm? Perhaps you should check file uploads. Some file upload modules will upload to the sites/example.com/files directory for your Web site while others might load to the sites/all/files directory. You might want to sort that out if you are creating several Web sites using multisite and plan to later move some of the sites to separate accounts for use with SSL.
Check your Web hosting account for SSL and IP address usage. Some of the lower cost accounts use one IP address across all the accounts on a server, removing the option to use your own SSL certificate. Some accounts make it difficult to upload certificates and perform related changes.
Using cPanel/WHM/Webmin or similar? Some of those control systems let you define multiple IP addresses and upload multiple certificates. Your Web hosting supplier might turn off some of those options and might have an external limit. They might place 20 hosting accounts on a server than can have only 2 IP addresses. Check the IP address depth before leaping into an account.