I have the same problem. I almost never use standard Ctrl-C copy, so when I am copying from a single-layer file I try Copy Merged and find out that it did not copy anything when I go to paste. Copy Merged should work on flattened files.
At a minimum, it should warn you that Copy Merged will not work on flattened files, rather than doing nothing at all.
This is a bug that has been around for years and years. Please fix it Adobe.