A lot of more complex sites make use of subfolders in the muplugins folder, just like with regular plugins.

They then use something like the Bedrock Autoloader or the MULoader in WPStarter.

Although these plugins are then active like normal plugins and properly shown in the WP admin backend, WP-CLI does not display them with plugin list.

To correctly mirror WP behaviour, these should be shown as well if they are active.