No worries Rob,
I checked with @Osama and indeed, the query would only show those who’ve set a theme in their preferences that’s different from the default on your site.
It also includes those who’ve changed back to the default theme after choosing some other non-default theme.
For all intents and purposes, all users that the query returns that use the default theme + any users that don’t show up can be counted as users that use the default theme.
The query will also return a breakdown of the number of users that chose any other user-selectable themes on your site.