I think this just about deserves a confidence 3, but no more. I found quite a few examples of the expression "Notario suplente del titular" in Chilean docs. In fact there's been a KudoZ question on it, with the answer "alternate notary public".
http://www.proz.com/kudoz/spanish_to_english/law_patents/289...

If it were "N.S.", I would say it would very probably be the answer. But "M.S." must be something else.

I just remembered that notaries' assistants used to be called "ministros" in Spain in earlier eras. On checking Chilean sources, I find that "ministro de fe" denotes the prime function of a notary:

"1. El papel del notarío
El notario es un ministro de fe. "Es un funcionario público autorizado para dar fe de los contratos, testamentos y otros actos extrajudiciales, conforme a las leyes""
http://mingaonline.uach.cl/scielo.php?pid=S0718-095019910001...

And again, we've had questions on "ministro de fe" in Chile, for which "authenticating officer" or "certifying officer" seem to me convincing translations:
http://www.proz.com/kudoz/spanish_to_english/law:_contracts/...
http://www.proz.com/kudoz/spanish_to_english/law_general/281...

So I would suggest that M.S. could stand for "Ministro (de fe) suplente".

It could be that the person is not him/herself an actual notary public, but is acting as an authenticating officer as an alternate to the incumbent notary. I don't know about that. But it seems to me a reasonably plausible possibility for "M.S.".