I’d prefer to see the /acf-json/ directory and files located one level up in the /wp-content/ root.
Perhaps still also looking in the /theme-name/ directory as a secondary lookup if not found in /wp-content/ to preserve backward compatibility.
This would be in-keeping with other plugins that do this, like:
Saves in > /wp-content/config/
Custom Global Variables:
Saves in > /wp-content/custom-global-variables/