I've struggled with the same problem. A long time ago I noticed that
standardized spelling helped enormously in finding people and matching
duplicates in my database. So now I've standardized nearly all
surnames and given names, even being careful with the accent marks.

But in the source citations I do the best I can to preserve the
original spelling as found in each source.

I also record pre-surnames like "de la" in a field that isn't involved
in sorting yet does appear in printed reports: so that de la Cruz and
Cruz sort together. I do the same with José and María, so that José
Antonio sorts with Antonio and María de Refugio sorts with Refugio. I
also expand abbreviations like Igo for Ignacio and Rdz for Rodríguez.

I think the important thing is that, to be an accurate transcriber,
the original spelling as found should be documented somewhere in your
database or research notes.

Many scribes make no distinction whatever between g's and q's, so much
so that there seems to have evolved two forms of some names. Like
Vásguez and Vásquez. Whenever I see these I always assume the more
common form -- until I'm informed otherwise ...

And of course everybody probably knows by now the interchangeability
of S and Z, J and X, V and B, C and S, H or no H, and a few other
combinations.

One problem I am still dealing with, not being a native of Mexico, is
diacriticals. Rodríguez is almost never accented in handwriting --
probably because it is so common -- but to strictly follow the Spanish
accent rules, the accent must be placed, unless it is spelled
Rodrigues, in which case the accent mark isn't needed. Since many of
these name are not familiar to me, I often mispronounce them. I've
only recently learned, for example, that Julian is properly pronounced
(and written) Julián. So from time to time I pick a certain given name
or surname and go through the database and correct the accent marks.

(For any who are not familiar with the rules, Spanish words are always
accented on the last syllable, with only 3 exceptions -- unless it
ends with S, N, or a Vowel. If it ends with one of those it is
accented on the next-to-last syllable. If it is pronounced any other
way, an accent mark is used to specify how it is to be pronounced.
There's another rule about what to do with words that end in two
vowels, but I'm a little fuzzy about that one.)