The signage declaring the old Santry Bypass to be N1 was newly erected when it was downgraded from motorway status. Ignoring fossil signs is not the same as going with newly erected ones. For the record, I don't enjoy the fact that the paperwork is out of step with the ground truth, but OSM practice is to go with ground truth in cases of real ambiguity. Signs on the ground can be manifestly wrong or they can be outdated, and it's reasonable to overrule those. But the only reference we have ever seen to the existence of a non-motorway N50 section is in the document you mention. If N50 were the number, highway=trunk would still be correct. And it would leave us with an annoying bifurcation in that route, since N/M50 also runs through to the port in the tunnel.