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Macguru is correct, in my experience you do not want the to be orphaned or left to stand alone, they do not get their strength from that. So, to take your question a bit deeper, first make sure you have the internal linking correct. If set up correctly all the pages within the sub-domain or canonical can be linked together. If not and they are not on theme then something isn’t right and you want to look at that. You will also want it legitimately linked to and from the homepage and then from any other canonicals within the structure of the site that relate.
Once you have this internal linking built in strongly so the site is supported you can begin to look for linking partnerships, make directory submissions and find themed portals or vortals that support your separate canonical themes. In essence then your whole network grows, not the specific canonical.
>…would see a link to www.subdomain.mysite.com as a link to www.mysite.com and vice versa…>
No, in most cases they are looked upon as separate sites but, if the internal linking is strong and correctly implemented than the canonicals will benefit from the separate incoming links they each receive.
>… if the sub domain was given 20 links from sites relevant to its topic and the main site on the root domain is granted 20 links from other sites relevant to its topic would it count as 40 links in total or are they counted separately…>
In simple terms, no. If implemented as Macguru and I have suggested than as a whole, yes.
If you are developing a site with canonicals then make them work for you. If you do not tie them in correctly you can actually lose benefit from them. You would be dealing with several sites and not one strong network. Good luck, I hope this helps.
I did this before for a huge portal wich main domain benefited from 12k plus inbound links. Not for those to get lost, we kept the old version on line and redirected all those old pages to the appropriate new main section page. I took 3 months for the team to prepare this, but the negative impact was minimal. In nearly 5 months we lost less than 2000 links. We are starting to gain new ones on sub and main domains more than we loose on main alone.
However, links from the main domain to the subdomain will probably be more sparse, and rather more integrated into the content.
As for links from subdomains to other subdomains, they'll be even more rare. Are these just as important? It should be possible to find an excuse to create great context appropriate links if so...
Although the inner linking wasn’t a part of your original question teresha, it’s a very important key to the process of developing link strength for sites using canonicals.
>…As for links from subdomains to other subdomains, they'll be even more rare. Are these just as important?…>
I feel they are very important, as long as they stay on theme. For one site I work with I have a dog canonical and a cat canonical and a health canonical. I do not link dog to cat or visa versa but I do link both to health.