I think that adding a button like “Check Entities IDs” or maybe even do it automatically every X hours and notify if it found some Entity ID used in Automations\Scripts\Other Places but doesn’t exist anymore could really help.
Sometimes you change or delete entities\devices and you don’t have a friendly way to change\remove all the references of this entity\device.
A few times I have been editing old conditions only to find an entity that I’d deleted ages ago,
The only issue I see is that having this enabled by default on restart would cause issues if you had just created some new input helpers used in a new automation and not reloaded the helpers first.
I wouldn’t want this to be automated for that very reason. More than once I’ve been in the middle of doing something and the power will go out or something else will cause my instance to go down. Having this automated would kill me in that regard.