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Will go with separate self contained installs as the performance gain is negligible. Wordpress upgrades are straightforward so the maintenance gains are also negligible.
References
Determine if this actually increases security - http://www.suphp.org/Home.html. It seems to make the most sense for shared hosting.
This article indicates that suphp is slow as it makes php run as a cgi. Instead it recommends restrictions using mod_php - http://serverfault.com/questions/279938/should-i-use-suphp-or-mod-php-for-shared-hosting. Along this thread another poster recommends, http://mpm-itk.sesse.net/ which allows vhosts to be run under different uid and gid.
This restricts the php process to specific directories - http://help.godaddy.com/article/1616