I’m just assuming here but this is usually done by fingerprinting for specific version files/directory’s/code and sometimes even size.
For example you can remove all the meta versions tags ( isn’t there like 12 places) and .txt file for 3.1 but since 3.1 is the only version to include the following new file by default, it is rather easy to fingerprint.
wp-includes/js/l10n.js
Since each release has many new additions, if you spend enough time writing a smart bot, it not very hard to find release specific data. Hiding all this info would be a lot of work for every release.