I was about to post that no, the PCI version had the older AKM DAC chip in it, but checked the E-MU site and discovered that the newest 0404 PCI's apparently have indeed been upgraded to the newer AK4396 chip......which was not available when the 0404 PCI was initially introduced.
According to that page, the "new" 0404 PCI uses the Burr Brown/TI PCM1804 ADC and the AK4396, while the original version used the PCM1820 and AK4395, respectively, according to a review of the PCI card back in 2004 in Sound On Sound.
EDIT: When I tried to find data on the "PCM1820", Google only showed the hits from the Sound On Sound article. Turns out that article has a typo; the original 0404 PCI used the PCM1802. What that all means is the original card had 24 bit/96 kHz capability, and now it has 24 bit/192 kHz capability with the new chips.
I'd bet there is going to be quite a bit of confusion on this one, because it was more or less common knowledge for quite a while that the 0404 USB had entirely different DAC's and circuitry than the original 0404 PCI. The "0404" portion of the name was never meant to imply any commonality (other than the number of inputs and outputs) between products that had differing interfaces.
So now, that is a good question. One of the biggest advantages to the USB version would be isolation from interference in some PC's. With no file playing, try turning up the volume to max on your headamp. Do you hear any buzzing, humming, static, repetitive "zip-zip" or squeaky sounding noises? My Chaintech AV710 seemed to pick up quite a bit of that, and I hear none at all via my 0404 USB.
