How to display configuration updates when deleting fields programatically
As discussed in the comments the solution, in most cases, is to add the field storage to the config/install folder of the module specifying persist_with_no_fields: true.
core/modules/block_content/config/install/field.storage.block_content.body.yml
langcode: en
status: true
dependencies:
  module:
    - block_content
    - text
id: block_content.body
field_name: body
entity_type: block_content
type: text_with_summary
settings: {  }
module: text
locked: false
cardinality: 1
translatable: true
indexes: {  }
persist_with_no_fields: true
custom_storage: false

Then the configuration updates will be displayed when the module is uninstalled.
Sometimes the dependencies on the module disappear after configuration saves because Drupal is optimizing duplicate dependencies. Then enforce the dependency for this configuration item. See How to properly manage field types for a content type created by a module?