The compiler the IDE uses is gcc and it supports namespaces.
You might need to be careful with prototypes - I would not be surprised if namespaces and the IDE's process of defining prototypes for you could conflict.
Note that the Arduino function prototype generation system is only applied to the sketch files with .ino (and .pde) file extension. Sketch preprocessing is not done on libraries. So you have no worries about function prototype generation failures in libraries because there is no function prototype generation.
So the only concern would be if the library requires the user to directly use namespaces in function signatures in the sketch.