Ran into this one too, in a different way.
What makes it even worse: if you merge directories, it's MUCH more likely than 
usual that at least one of them contains symlinks into another. And then moved 
symlinks overwrite their own destinations. With files you at least retain 
something useful...
I just tested it meging two ".../test/" - destination contained a real 
non-empty subdirectory and source contained symlink to it with the same name. 
Oh, yes, nautilus does ask whether to overwrite. The problem: it asks this -

File conflict
Merge folder "1"?
Another folder of the same name exists in "test"
...

["folder" icon] Original file
Size:(null)
Last modified: 11:22

["folder" icon] Replace with:
Size:(null)
Last modified: 11:33

Which gives an impression that they are of the same type and both are
empty - while neither is true. Thus the user trusting the dialog is
going to confirm, and have the real directory overwritten with now-
broken link.

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https://bugs.launchpad.net/bugs/95854

Title:
  Folder is overwritten with a file with the same name

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