updateArticleCount.php counts all the good articles (content pages), then writes that number to the first row of the site_stats table:

$dbw->update(
	'site_stats',
	[ 'ss_good_articles' => $result ],
	[ 'ss_row_id' => 1 ],
	__METHOD__
);

It doesn’t touch any other rows, so if there are other rows, as would be the case when $wgMultiShardSiteStats is set (T306589), then the total number would now be too high. For example, on testwiki:

lucaswerkmeister-wmde@mwmaint1002:~$ mwscript updateArticleCount.php testwiki; sql testwiki <<< 'SELECT ss_row_id, ss_good_articles FROM site_stats'
Counting articles...found 4816.
To update the site statistics table, run the script with the --update option.
ss_row_id	ss_good_articles
1	487
2	482
3	481
4	481
5	480
6	481
7	480
8	481
9	481
10	482

There are 4816 good articles at the moment (both according to updateArticleCount.php and when you sum up all the ss_good_articles values). If I ran the script with the --update option, then the table would afterwards look like this:

ss_row_id	ss_good_articles
1	4816
2	482
3	481
4	481
5	480
6	481
7	480
8	481
9	481
10	482

And the total would now be reported as 9145. (In general, if the rows are equally distributed, then the reported number would be 90% too high.)

This is probably mostly irrelevant, because $wgMultiShardSiteStats is only recommended for wikis that are so large that you probably don’t want to run updateArticleCount.php anyways.