Hi Niall,
The coordinate system exists to define how a coordinate relates to the physical world. For example, if you have a coordinate with the standard name "projection_x_coordinate" you don't know how to relate that to the real world until you know which projection has been used, what the parameters of the projection were, etc. This is still true even for "latitude" and "longitude" coordinates, as the definitions of latitude and longitude depend on an idealised shape of the Earth. (Granted, the different idealised Earth shapes generally only result in small positional differences which are often ignored.)
So, the ideal solution would be to track down the missing coordinate system information. (Where have these cubes come from?) But if you aren't concerned by the potential for small positional discrepancies then go ahead and create a coordinate system anyway. Either by choosing a simple default (e.g. GeogCS(iris.fileformats.pp.EARTH_RADIUS)) or by copying from another cube.