Assigning the right license to the right subdomain My client has 3 licenses, one for each of 3 subdomains. Let's call them A, B and C.
C has been derived from B, so has inherited B's license.key. How should I assign the correct license to C? Or does it not matter as long as the appropriate number of licenses have been purchased?
On a related note, my client's id.craftcms.com log stores the same root domain against all of them, so I have to put a reference to the subdomain in Notes. Not a problem as such, but the same domain for all seems  a bit imprecise.
Technically 3 separate Craft installations would require 3 separate/unique Craft licenses even if they share the same root domain (site.com) and live off in subdomains off of that (a.site.com, b.site.com, c.site.com).
If any of the sites are using the same config/license.key file, you could delete the duplicates and load the updates page in the control panel. A new one tied to Craft Solo will be generated and you can purchase Craft Pro updates for each individual site.

Not a problem as such, but the same domain for all seems a bit imprecise.

It's a bit ironic in your case because the reason we currently only track the root domain is to let all subdomains of that root domain be able to share a single config/license.key file for a single Craft installation in a multi-site setup.
Using the notes field in your Craft ID account is probably be best way to keep them sorted.