in my case, wp 3.9 auto update also broke my wp multisite install, and i have subsites on subdomains. Now subsites redirects to default cpanel page, and subsites can’t be accessed from the admin area as /wp-admin/ for subsites brings:
404 Not Found
The server can not find the requested page:
/wp-admin/ (port 80)
my fix was suggested by my host: while the domains in the wp network worked for years without adding child sites domains to cpanel, after a cpanel update i had to add them as addon domains in order to have them work, and fix the “bug”. I understand this is not WP related, and may not be your problem, but felt obliged to report it.