I think you are reading more into Chrome's behavior than is warranted. In general, there is little reason to believe that software is actively malicious. You are also using hard links, which can have somewhat unintuitive behavior in edge cases.
Specifically here, a common way of making writes at least semi-atomic is to rewrite the contents of the file under a new name, and then move the new file into the old file's location.
As a step-by-step process, this can look like this:
- Generate a random file name that does not exist in the intended target directory
- Create that temporary file
- Write the data to the temporary file
- Rename the old file to a different name
- Rename the temporary file so that it has the same name as the original file
- Delete the old file
This process ensures that at all times, at least one valid copy of the data exists on disk. Hence, even if the program crashes half-way through, it's easy to recover to a known valid state.
However, as a consequence, step #4 breaks the hard link, and step #5 puts something else under the same name.
If you simply want to be able to access your bookmarks file under a different name, I suggest simply making that other name a symbolic link to the bookmarks file.