I was under the impression that the default [Black] always overprints, but in this kind of layout, if the bitmap placed in the K layer, with [Black] fill, is not set to overprint, it knocks out the images below it with Y, M and C fills (fills of Y and M also set to overprint). So here is the corrected script:

tell application “Adobe InDesign CC 2017”
tell document 1
try
set theImages to all graphics of layer “C”
repeat with thisImage in theImages
set the properties of thisImage to {fill color:swatch “C=100 M=0 Y=0 K=0”}
end repeat
end try
try
set theImages to all graphics of layer “M”
repeat with thisImage in theImages
set the properties of thisImage to {fill color:swatch “C=0 M=100 Y=0 K=0”, overprint fill:true}
end repeat
end try
try
set theImages to all graphics of layer “Y”
repeat with thisImage in theImages
set the properties of thisImage to {fill color:swatch “C=0 M=0 Y=100 K=0”, overprint fill:true}
end repeat
end try
try
set theImages to all graphics of layer “K”
repeat with thisImage in theImages
set the properties of thisImage to {overprint fill:true}
end repeat
end try
end tell
end tell