The Apogee Duet is only 2in 2out. It should be fine running on the same Firewire port as the external drive you're recording to, even at 24 Bit 96 KHz. If you 'd be recording 8+ channels, it would be an entirely different story.
Don't know why you think that would be a different story.
Because of the way isoch works, with ideal interfaces, FireWire 400 should be able to reliably handle 377 channels of 44.1 kHz audio, which can be any combination of inputs and outputs. Realistically, audio interfaces tend to request a bigger time slice than they need, so you may end up maxing out the bus with as few as a hundred total channels, IIRC. (Yes, I've hit that wall experimentally just for fun.) Even still, that's a really big number.
Now a FireWire 800 port has four times the bandwidth (full duplex 800 Mbps down, 800 Mbps up instead of half duplex 400 Mbps shared between upsteam and downstream). So think about sending somewhere between 200 and 700 channels of audio in each direction at the same time. Now ask yourself who in their right minds would do such a thing.
In theory, it might be possible to run out of FireWire 800 bandwidth when doing audio. In practice, you'll hit a disk speed bottleneck long before you get there, not to mention a CPU bottleneck handling the channel mixing, a RAM bottleneck holding your buffers, etc.
In other words, yes, you can safely daisy chain the devices. I suggest putting the FW800 device first if possible so that your hard drive doesn't end up being forced down to FW400 speeds. Either way, it should be fine.
