If your nozzle is worn enough that you can't read the size stamped on one of the hex flats, you need to replace it anyway.
That said, the best ways I know to measure the aperture are with either a pin gage (known diameter high precision wire, find the largest that will enter the nozzle aperture), or optically -- take off the nozzle or hot end and put it on a scanner bed; use the scanner to image the nozzle at highest available resolution, then count the pixels across the opening in the image and multiply by the pixel size (for instance, if 6400 ppi, you'd multiply your pixel count by 1/6400 in/px * 25.4 mm/in).
I've used the optical method to measure photographic pinholes (drilled in delicate, .001" thick brass shim stock) that were smaller than 0.5 mm, so I know it works in this size range.
Measuring the extruded filament may not give an accurate diameter, for two reasons -- the hot, freshly extruded material may either swell or stretch after extrusion (and may well do both in a short length of extrusion, giving varying diameter), and it's difficult to accurately measure small round samples (especially of plastic) with either micrometer or dial/digital caliper -- it's too easy to compress the sample and obtain an artificially undersize result.