Basic REST and JSON RPC are very simple to start with, but have common problems when application gets bigger. How do you represent relations, pagination, filtering etc? My go-to specification for structuring JSON documents is https://jsonapi.org/ It covers most basic needs of a standard API.
Schema(or data in a database) in your release N should be compatible with release N-1, so you can revert your code to previous working version with new schema. That's the only way to ship new releases without stopping service for maintenance.
A lot of replies talks about schema migration and tools like Liquibase etc. But as I understand the question, it's about running update / delete queries in production environment, not DDL.
In my opinion such queries should be subject of established development process:
1. Commit your query to a repository
2. Send to code review
3. After successful review and merge it should be deployed automatically by ci/cd
It may be necessary to run query directly via console in some cases, though. But such query should be committed to the repository latter any way.
And of course you should use proper tools like comments suggest.