I'm exceedingly doubtful you could do this with a netduino at any sort of decent speed.
Initially you need to get another USB port from somewhere at minimum, but likely 2 as they need to be host ports. Either these would have dedicated controllers of their own, which you interface with over SPI or I2C or something, or you'd need to bit-bash them, the second likely isn't possible at all due to timing issues, the first would severely limit your speed.
Secondly you don't have the sort of memory available for to do any sort of decent read caching. Assuming you can pull that off, you then need to be able to decode the partition table and file system, read the data from it and and write the data to the new file system at ~30MB/sec whicih is all you can get from USB2 anyway. I don't know of any way you could push that sort of speed through a netduino alas.
You dismiss the software as easy, but being able to read and write to NTFS partitions and file systems is no small feat for something on this scale.
For something like that you'd probably want to look at something like an FPGA board, but even that would be pretty painful as while you'd get the hardware side done fairly easily at decent speed, you still need the whole filesystem and partition layer to be able to write to the second drive.
