Reading through the documentation you have the ability to setup a WP Network in two ways, Sub-Domains and Sub-Directories. The only explanation they give you is
Sub-directory sites
It works with the use of the mod_rewrite feature on the server having the ability to read the .htaccess file, which will create the link structure.
If you are using pretty permalinks in your blog already, then subdirectory sites will work as well.
Sub-domain sites
It works using wildcard subdomains. You must have this enabled in Apache, and you must also add a wildcard subdomain to your DNS records. (See Step 2 how to set up.)
Some hosts have already set up the wildcard on the server side, which means all you need to add is the DNS record.
Some shared webhosts may not support this, so you may need to check your webhost before enabling this feature.
I’m looking to find if there is a performance, maintenance or other benefit to use one over the other.
4 s
I began using Multisite just a few months ago, and am really loving it. You’re going to want to use the sub-domain structure if you have a host that supports it. I use a Media Temple Grid Server plan. It will allow you to create a subdomain and then mask it with a symbolic link. i.e. rtgibbons.mynetwork.com would be mapped as rtgibbons.com or whatever URL you want presented.
Upon a Google search, I found that as long as you plan to use Domain Mapping, there will be no advantage to either method.
http://wordpress.org/support/topic/multisite-subdomain-vs-sub-directory-setup?replies=4
I’d suggest subscribing to the WordPress.org Multisite Forum. There is very good info over there and Andrea_r is very sharp.
