The theme.json currently does not serve a purpose beyond acting as a template.
The contents of theme.json is inlined into client.js and referenced internally so changing theme.json won't have any effect on your installation.
You can edit the theme.css however if you want to apply some css rules to your installation.
The files exist right now as we are preparing to launch theming in later releases.
The default theme.json from "C:\Program Files\Qlik\Sense\Client\themes\sense" is apparently not read by the server. Copy/paste the "sense" subfolder and give it your own name like "C:\Program Files\Qlik\Sense\Client\themes\mytheme" and add ".../theme/mytheme" to the url of the resource (e.g. http://localhost:81/sense/app/24d645c6-ca55-4dc9-ad32-000c685f38fc/sheet/df6a5/state/analysis/theme/mytheme.
If you modified the "theme.json"and "theme.css" in that copied folder "mytheme", then it will be applied (once per session at least, the rest is browser caching as well as server-side caching).
When working on Qlik Sense Enterprise:
If you want the default theme to use the theme.json in the default folder (C:\Program Files\Qlik\Sense\Client\themes\sense\theme.json), you can remove the hard coded define for "text!themes/sense/theme.json" at the end of the main require.js file:
Hope that helps!