Hi @magikCT, @hello - good news 
I have a solution to the problem. It was staring me in the face. As part of another project I had some AppleScript that was really easy to modify so it performs the task of deleting disabled actions in a macros, regardless of how "nested" they are.
This is the AppleScript file:
Delete all Disabled Actions.scpt.zip (2.9 KB)
Download it and unzip to somewhere on your Mac.
Then create your "Delete all disabled actions" macro in KM with just a single action to run this AppleScript file, like this:
(Point the action to wherever you saved the AppleScript file - I put the file on my Desktop just for simplicity when testing.)
Here's the macro I used:
Delete All Disabled Actions.kmmacros (2.4 KB)
Please note: because the AppleScript code is part of a larger system I am developing I can only provide the runtime (i.e. non-editable) version.
The code itself is quite complicated and so may take a few seconds to complete the task you set it. You could add a Play Sound action at the end of the macro to tell you when it has finished!
The usual caveats apply: this code is destructive and while I have tested it without any problems you should use it with care and make a copy of any macro you use it on first!
If you try this out let me know how you get on.