What would cause edit buttons for plugins to disappear?

Edit buttons display only when the necessary file permissions are acquired by PHP.

http://core.trac.wordpress.org/browser/tags/3.3.1/wp-admin/includes/class-wp-plugins-list-table.php#L380

is_writable(WP_PLUGIN_DIR . "https://wordpress.stackexchange.com/" . $plugin_file)

current_user_can('edit_plugins') will always return false if the DISALLOW_FILE_EDIT flag is set to true (recommended) in the configuration, no matter if you’re the administrator or not.

http://core.trac.wordpress.org/browser/tags/3.3.1/wp-includes/capabilities.php#L1118