I just checked the DA-40 POH (for the 1.7 Thielert-engined version). Indeed it's only got one (90A) alternator, but it's got no less than three batteries in the VFR edition:
- Main battery 12V, 35h Ah
- Alternator excitation battery 12V, 1.3 Ah
- ECU backup battery 12V, 12 Ah (powers ECU-B only)
The ECU backup battery should supply power to the ECU, if all else fails, for at least 30 minutes.
The IFR models also have a non-rechargeable dry battery to power the cabin floodlight and (electric) AH for 1 hour, completely independent of the electric system.
Now I'm not an electrical engineer but, although complex for such a small aircraft, the electric system of the DA40 does seem to be well thought out. My main worry would be if a failure elsewhere plus a failure of a critical relay to open/close a circuit somewhere would occur. For instance a short in the main bus, and a failure for the relays to isolate the ECU bus. Or something along those lines.