API access to custom fields
Due to the fact that ACF stores the values of custom fields in Shopify metafields, you can leverage Shopify's API for handling those metafields to update any field value inside ACF.
The field values for the various Shopify objects (shop level included) are just normal metafields with the namespace and key as defined by you in ACF.
Using Shopify's API you can create, update and delete metafields as you see fit, but:
To ensure ACF keeps working with any content you create or edit outside ACF itself, please respect the metafield data type and content restrictions for each field type.
Also, the general ACF rule stating that if a value of a custom field is empty, its corresponding metafield does not exist should be adhered to.
ACF's internal field definitions are stored as shop level metafields in your store with some special namespaces unique to ACF. For uninterrupted service by ACF, don't update these metafields via the Shopify API.