Table 'menu_custom' has been removed, and information about custom menus are now configuration. Each custom menu saves configuration to a separate config file named as menu.menu.MENU_NAME where MENU_NAME is the name of the menu.

Example:

// D7 code
$row = db_select('menu_custom')
      ->fields('title')
      ->condition('menu_name', 'main-menu')
      ->execute();

// Backdrop 1.0.0 code
$config = config('menu.menu.main-menu');
$config->get('title');

Alternatively use function menu_load_all() to get data about custom menus.

Introduced in branch: 
1.0.x
Introduced in version: 
1.0.0
Impacts: 
Module developers
Theme developers
Related Github Issues: 
https://github.com/backdrop/backdrop-issues/issues/653