just to make sure I understood your issue: You have a device running linux, that has 17 USB ports. The purpose of this device is to make a copy of usb mass-storage devices attached to the master USB port and write those copies to the slave USB ports?
There should be no problem in doing a bit-to-bit copy of the disk contents, as long as the final disk is at least of the same size as the source disk. I assume that the disks have a DOS partition table and that there are one or more partitions on it. If the final disk is larger than the source disk, there will be just unallocated space on the disk, that can be used, if the partition table of the final disk is modified afterwards, but not necessarily. So in this situation there should be no problem.
If the final disk is smaller than the source disk, then you can have serious problems, because you cannot store all information on the final disk. Your technique will yield an invalid paritition table and this means that it contains partitions, those boundaries may lay outside the disk. In this case, the filesystems may be usable, but need not to be. Partitions, which totally fit onto the final disk, will work as before.
So you can either copy only certain partitions (note: NTFS partitions need to start at the same position on both the final and source disk!).
Another possibility is to mount all partitions on the source disk and create them on the final disks such that all files will fit in them. Then copy only the files. This method is better and more robust.