Keanna here from the Better Reports support team.
I believe our app Better Reports can help! You can create a custom report showing all collections that have ZERO products associated with them. This will help you identify the collections to be removed from your store.
In addition to building custom reports to meet your specific needs, you'll have access to 60+ built-in reports that cover many common use cases for merchants and our reports can be scheduled to send to your email or Google Drive at set frequencies - like after the close of every day.
I encourage you to install Better Reports and start your free 14-day trial, and I'll be happy to set this up for you.
Let me know how you go and feel free to reach out if you have any further questions.