the games ran too slow for me, so i gave up on dreamcast emulation on the pi3 a few months back. i ran into this same problem and can't remember exactly how to bypass it, but there's some helpful info here: https://github.com/RetroPie/RetroPie-setup/wiki/Dreamcast#bios
Note: If you are having trouble with having to set the date/time every time you load Reicast, see this forum post for a guide on how to replace dc_flash.bin. The MD5 of the dc_flash.bin generated from that guide should be 2f818338f47701c606ade664a3e16a8a
also, the relevant section of my emu.cfg looks like this:
[input]
evdev_device_id_1 = 2
evdev_device_id_2 = 3
evdev_device_id_3 = -1
evdev_device_id_4 = -1
evdev_mapping_1 = /opt/retropie/configs/dreamcast/mappings/controller_LogitechGamepadF710.cfg
evdev_mapping_2 = /opt/retropie/configs/dreamcast/mappings/controller_LogitechGamepadF710.cfg
joystick_device_id = -1
make sure the controller cfg file exists and the contents are correct (should match up with the ones in /opt/retropie/configs/all/retroarch-joypads/).