You shouldn’t develop with your live server as active target. Also develop locally and when done and tested - then just deploy at once.
Custom queries take a full round trip to the server to execute them. In NodeJS world this will also result in restarting the server first. So if you do that on your live server it means that it have to be uploaded, server restarted, then executed etc. Which can take a while and is not very good for running on production server.
That is why we are also considering to prohibit editing server connect action on live targets as well, to also avoid the risk of accidentally breaking your live site.
As said always develop and test locally and when done publish at once to the live remote.