The Alabama Confederates who were discharged on account of having 'mixed blood' certainly could have applied for veterans pensions after the war. I'm sure the number I've come across are just a small portion of the larger total.
No matter what, we're never going to know the actual number of Confederates enrolled during the war. It would be equally difficult to determine how many men of 'mixed blood' (anything less than 100% causasian) served in Confederate commands for any length of time.
Ed Bearss stated that a limited number of women served in Confederate ranks, and a similarly limited number of black men did the same. Actuals counts of both must have been small, but there's really no way to know exactly how many there were. That's about it.