In Europe you will not get an ISO 13485:2003 certification anymore supporting CE marking, because the harmonised standard is now EN ISO 13485:2012. This is the only standard that gives presumption of conformity to the 93/42 EEC Directive.
The differences with the 2003 version are contained in the new Annex Z.
This is why Sabrina got a non-conformity for not having a copy of the EN ISO 13485 standard.
The standard version that applies in each area (EU or outside) is determined by the country specific medical device regulations.
So for EU it is EN ISO 13485:2012, for Canada it is CSA/ISO 13485:2003.
I understand your points but I partly disagree.
To get EC certified you don't have to be EN ISO 13485 certified. Harmonized standards are voluntary, and you are at liberty to show compliance with the MDD by alternative means. Since the normative parts of ISO 13485:2003 and EN ISO 13485:2012 are identical, a manufacturer certified to ISO 13485:2003 could argue that they are in compliance with the MDD (based on the fact that compliance with EN ISO 13485:2012 is considered equivalent to compliance with QMS aspects of the MDD). Some NBs might not accept that argument but in my opinion that would be unreasonable and unfair. On the other hand, I think that there are at least a few NBs out there that would accept (and it's not because they're inferior or slack). All this is to say that the EN version is required for presumption of conformity, but presumption of conformity is not the only route for MDD compliance and EC certification.
Annex Z is part of the informal part of the standard. It shows how the standard satisfies MDD requirements, but it's absence doesn't prevent compliance with the MDD.
I don't know why Sabrina got the NC for not having the EN version, I wasn't there and I don't know what argument her company made. If they somewhere claimed compliance with EN ISO 13485 while not having a copy, that could be a reason. However, simply not having it is not a justified cause for a NC because nowhere in the MDD it says that you
must have it or comply with it (or any harmonized standard).