The D-Star code squelch information is transmitted within the slow data section of the DV transmission. It has it's own ID (0xC2 I think, and the code is repeated twice for a little robustness). Since it's in the slow data section, code squelch data should pass through the D-Star repeater network unmolested.
For those interested in protocol information, the code squelch data number is converted to binary in an odd way, a value of 12 on the screen will be transmitted as 0x12 in the data stream! Jonathan G4KLX