While I have yet to locate photos of poultry cars loaded on the Santa Fe in SoCal, I feel it is highly likely... at least in the 1920 & 1930 with Thanksgiving turkeys from Ramona.
Ramona, CA was once known as the "turkey capital of the world" and I learned they originally had annual "turkey drives" where the town would get together to drive flocks "to the station". This informal parade & season ending celebration evolved and by 1933 the event was formalized and popular with tourists till the last one in 1941 as WW2 cancelled the event. At some point, the turkey drives died out, replaced by trucking.
Live turkey from Ramona were shipped all over the US. There is a local rumor that President Woodrow Wilson once pardoned a Ramona turkey at the White House, but others think it was Truman and still others think it was neither. But the real mystery to me is what "station" was the destination of the original Ramona drives, as the town isn't on the track. My theory is the first drives would have been to Escondido, CA, some 15 miles away, down the San Pasquale Valley.
I'll make some calls to see if I can confirm...