I was thinking [empeg serial] -> [serial <> USB multiplexer].

Considering the fact that most serial applications for in the car run at moderate speeds (4800-9600) and the empeg's serial can push up to 230Kbps without any special hacks, the bandwidth issue shouldn't be that bad. Timing issues maybe, but that is what the usb host controller cpu should solve.

I was mostly hoping there was some cheap embedded CPU with an USB host controller, but it looks like most embedded CPU's with USB only have a device controller.

But the fact that serial -> serial mux would require special kernel hacks anyways, and then we're still limited to the fixed number of serial ports that the hardware supports, with usb it can scale moderately. Also considering the fact that a max233 is between $5-10, so a usb dongle is not that much more expensive.
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40GB - serial #40104051 gpsapp