I don't think it matters as long as the area of the hard disk you are using dd on has an operational Linux which may try to update the files during the dd operation.

The dd command actually copies the binary sector by sector and the file system is not involved at all, except as an output file first and then used in the second part as the input file. dd copies the boot sector as well.

Sorry for the late reply but I am currently holidaying between Australia and Hong Kong.