If I could have removed the offending nail, I would have. The heads are set well below the surface so there's no way to grab one for prying out.
I encountered problems on my old boots also during the blade testing. One of the permanent mounting holes on a blade interfered with a nail in another location. Because they've done it that way for 73 years does not make it a good engineering solution.
Sorry, I got a little grumpy there.
Nails have been used in shoes for centuries, at least. See
the Honourable Cordwainers' Company library website. Tradition! But most shoes don't need to have skate blades mounted to the bottom. So maybe the tradition should change.
Obviously you might be able to pry a nail out, if you damage the nearby surface, by punching a small hole next to it (perhaps with another nail, at an angle), and then levering it out. But it isn't right that you should have to go that far, or mess up the surface that way. Also, if they apply adhesive to the nails or in the holes, the nails might be hard to remove that way
If they used screws instead of nails, and used no adhesive or only an adhesive that breaks easily, they would be easy to remove. However, it would add extra seconds to production time and require new equipment.
If they applied all the nails at the extreme edge of the sole? Though maybe that wouldn't apply enough pressure in the center to let the glue set... Or maybe the direction of the leather grain isn't right in the uppers to hold the nails?
If you got grumpy, I bet other people have had the same problem. You have nothing to be sorry for - they do. You are probably right, and they should fix this, one way or another.