This happens when you run a script (AppleScript, Shell Script, etc).
As you know, the variables are placed into environment variables, with names that start with KMVAR.
However then total space for the environment variables is limited (by an unspecified limit, sigh), and if the total size of the environment variables exceeds this limit, then the script will not run at all (the attempt to start the script will fail). So Keyboard Maestro takes care to ensure that the total size of the environment variables it includes total up to less than around 100k. If the total size of all your variables (which includes non-password variables, local variables and instance variables) exceeds 100k, then the largest of them will be omitted.
The notification in the log is so if that happens to be a variable you really want to access, and it is not there, you have a change of figuring out what is going on.
You can always access larger variables via AppleScript to the Keyboard Maestro Engine as normal.
So no, you don't have to take any action to prevent these log entries and unless you need to use those specific variables in your scripts, you don't need to do anything.
I trust that is clear.