Oh, Wow, I think I may get it???
This has an RS-232 Serial input/output! So those signals swing both + and - (or they need to to be compatible with most all serial ports on whatever computer.)
So: Where does any negative voltage come from, anyway??
When the RS-232 Receive Data (DB-9 pin 3) is "Marking" ie not sending (and during the Mark pulses on normal data), D3 charges up C9 to a negative voltage (Whatever the connected computer's RS-232 driver puts out)..
Mmmmm...
When the Arduino is Transmitting to the attached computer, T2 swings RS-232 Transmit Data (DB-9 Pin 2) from +5 (through JP0) to the negative voltage that C9 is charged to. Keeping the RS-232 Gods happy.
Ummm..
Received data also drives T1 who translates the RS-232 voltage swings to TTL (+5 to Ground) and it's base-emitter diode D2 clamps the negative swing.
BUT -- (An Official Engineering Event that needs to be considered)
IF wiring or something is messed up, or the Computer sends a RS-232 BREAK,
THEN C9 COULD go to opposite polarity. SO it would be safer if it was a non-polarized type.
I might have taken a different approach and put a diode pointing down across C9 to protect against that BUT. Easier to find than a non-polarized capacitor.
Hmmmm..
Other Opinions???
PS: Your "Just use a polarized capacitor" "Probably works, most of the time"..