Hi,
I think this is the same issue as PHP Warning but import works, just seen indirectly.
Explained in an abstract way (this is not Matomo code):
The PHP-cli archiving process makes some HTTP requests to the Matomo API for some things. If this works, it responds with something similar to this:
a:1:{s:7:"message";s:7:"success";}
php-cli then runs unserialize() to find out that this corresponds to this response and continues
["message" => "success"]
But due to your issue, the webserver responds with
PHP Warning: Module ‘mysqlnd’ already loaded in Unknown on line 0
a:1:{s:7:"message";s:7:"success";}
which then is an invalid format for unserialize() which means the notice is shown. As this is only a warning when parsing the result message, the archiving should still give the correct result.