Does your compositing node tree look something like this?:

Or do you even need to multiply the number of nodes with the number of scenes you have?

And you've also got a bunch of view layers in each scene?

If this szenario matches yours, then you probably need the Peacock Renamer Addon! It will save you hours of work structuring and renaming your project!!! 

Peacock Renamer Addon

The Peacock Renamer is an addon for Blender which lets you rename 'Scenes', 'View Layers' and the output paths of 'File Output Nodes' with the means of Regular Expressions.

Before you apply the changes you see an interactive list with all changes that will be made as soon as you click the rename button. You can exclude single items as you desire.

The 'Regular Expression Help' on the bottom of the addon might help you out when you're stuck with Regular Expressions. You can also search the Help and get a comprehensive list of only the infos you need.

The full list of all help items looks like this:

Regular Expression Help