All versions of the game (barring OD&D & Basic, which had no
familiars) had familiars being smarter than usual. In 1st Ed,
familiars are "abnormally intelligent". In 2nd Ed, they are "more
intelligent than others of its type, typically by 2 to 3 intelligence
points)". In 3E/3.5E, the PHB reads, "Familiars are as smart as
people, though not necessarily as smart as smart people." And in 5E,
while they don't actually specify intelligence since the familiar is
described as not actually an animal but "a spirit that takes an
animal form", we can assume it has greater-than-usual intelligence as
well.
So familiars have never been truly "natural" animals (and in 5th
Edition, aren't animals at all anymore). Thus spells that affect their
status shouldn't automatically negate the fact that they are a
familiar although, it might cause issues in the relationship between
wizard and familiar. The more intelligent the creature, the more it is
likely to recognize - and resent - unfair treatment.
As it says in 2nd Ed, "Deliberate mistreatment, failure to feed and
care for the familiar, or continuous unreasonable demands have adverse
effects on the familiar’s relationship with its master. Purposely
arranging the death of one’s own familiar incurs great disfavor from
certain powerful entities, with dire results."
But ultimately this is an issue I think the individual DM has to
determine for himself; he has to think of how he wants familiars to
act in his universe, what their abilities are and what restrictions
are placed upon the wizard. Just strive for consistency; for instance,
if you rule that a spell that makes a familiar more intelligent breaks
the familiar-bond, what about a spell that Enlarges the creature, or
Polymorphs it. Are familiars just normal animals that serve as "magic
batteries" or fey spirits? Don't depend on rules to explain the world;
it's a game of imagination, after all.