Is it 1/3 on each side or 1/3 in total?
1/3 of each side would be 1/3 of total, so yes.

Since this is a general recommendation for driver,does it apply as well for a co-axial or is there a correction to be applied when measuring the diameter of a co-ax.
Are you asking what to do about that portion that would be the dust cap in a typical woofer? I'd have to defer to the experts on that one.

.Added mass :I have tried to add masses to the back side of the cones but they dont stick long enough to perform the measure till the end.
Have you tried modeling clay, play-dough, silly putty, plumber's putty, rope caulk?

Can i use small magnets without affecting the results of the measures?
I doubt it, i don't think you can get the magnets located close enough to the voice coil without affecting the motor's own field or interacting with the motor's front plate.

Are you suspending the driver in a free field for your measurements? Nearby objects can cause reflections that will skew your measurements.