Why? It's people following a forensics script/program which looks for Windows partitions. There aren't a huge number of people who understand this kind of thing and most of them are able to work at places where they're paid much better than the FBI.
you would think that national level stuff would have people take more care, but if you're dealing with state or local police, they will have someone who has taken an 8 hours Encase or FTK class driving a GUI to gather evidence and if the tool doesn't support it, there's effectively no evidence to gather.
I guess it depends on whether the hard drives were the target of the raid or just a collateral of "grab anything that may be useful" mindset. They could already have gathered enough evidence without needing to waste time/money on digital forensics. Hard to say without specifics.
The fact that they went out of their way to assure him that his own hard drives were empty reeks of manipulation.
Color me highly skeptical.