As of #1399 and v3.0, a site's theme is set under the style attribute in site.json, and the theme attribute is considered deprecated. However, we currently still log a warning to warn the user against this, and gracefully handle the use of the theme attribute. (source code)
Let's fully deprecate the theme attribute, especially since we're moving towards v5. It's also unlikely that users are still using it since it's been undocumented since v3.