I've had a pretty close look at my BDA-1 -- there are 2 optical (toslink), 2 rca (spdif), 2 bnc (spdif), 1 xlr (aes ebu), and 1 usb input for a total of 8.
The 2 rca connectors could probably be replaced with bnc ones. The 2 optical, 1 xlr, and 1 usb inputs are likely not possible to replace with bnc without significant mods to the circuit board.
But Mike will know for sure.
None of the leds run through light pipes.... They are all soldered to the front panel circuit board and poke through the holes in the machined aluminum front panel. I've been told it's a real bitch to get them all lined up when installing the front panel

So I wouldn't get your hopes up for any modification for these....