Yes, it would affect the quality of the footage being transferred. To transfer XDCAM clips in full, original quality, you need to connect your PMW EX3 through the USB connection. The PMW EX3 can convert and output HDV through Firewire, but this is not going to be the same quality as the XDCAM video formats that the PMW EX3 is capable of recording (full 1920x1080i, 1080P or 720P at 35 Mbps, versus 1440x1080i at 25 Mbps HDV). By the way, you can also transfer XDCAM clips by inserting the SxS flash memory cards in the ExpressCard slot of your capable laptop PC.
That being said, I haven't tried it, but I would think that the HDV quality would be pretty good through the Firewire connection. As it would be HD, it would be much higher resolution than a Sony DSR 370 DVCAM camcorder is capable of providing.
Tom