Does the number of downloads displayed for a plug-in in the WordPress.org plug-in directory include automatic updates?

That’s the total number of downloads. It includes direct downloads in the Repository and installs/updates done in the dashboard.

Quotes from Otto comments in this 2010 article about the stats charts in every plugin’s page.

[…] the download count includes direct downloads as well
[…]
There is no “raw count” anywhere on that version number chart. The raw count is not data that will be made available.

From Ipstenu, in this forum thread:

The active version stats is from a ‘phone home’ feature, and I suspect it only updates when the blog’s update checker is run. Not everyone updates all the time.

An idea of the total sites using a plugin may be gathered comparing the Changelog and Statistics of a plugin, in this case WordPress SEO by Yoast:

wpseo changelog

Adding the daily download in the period of time after the plugin has an update until it reaches back its daily download average. And discounting that average daily number from the sum.
wpseo stats

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