With the caveat that I am not at all a carbon expert, I would say that if you have any sort of soil carbon data that you feel good about, you’re fortunate, since often we do not. So whatever the depth you have, it’s fine to use it, just note that depth when reporting the results.
This is also related to thinking about the “belowground” carbon pool, which theoretically can go as deep into the soil as plant roots, which of course varies by species. If you’re considering how changes to agricultural management are likely to impact soil carbon, I’d do some research into how deep those impacts tend to be found (different by crop type? root depth? other factors?), and work with that depth if you have the data to support it.