Junior / The Younger

In 15th-16th Century research I've come across several instances where
someone called either "Junior" or "the younger" is not a son, but a
younger brother. I even came across one where it seems to refer to a
cousin.

In your experience, how often is "junior" or "the younger" used for
someone other than a son?

Denis Beauregard...

I have seen that for 2 unrelated priests, 19th century. Having
both the same name (I think it was Joseph Beauregard), they used
that sr/jr suffix to distinguish themselves.

So, in a general point of view, jr/the younger and equivalent in
other languages can be any persons and is probably not enough
alone to decide they designate brothers, father and son, cousins,
or any other relationship. You can probably use that as a basis
for a work hypothesis and if the older or senior is not viewable,
I would say this is a father/son relationship, but if you can see
both of them in the same area at the same time, then it can be
any relationship.

As for statistics, there is just not enough vital records of that
time to have them. I think most of material for that is a set
of guesses.

joe...

Extremely often anytime before the 19th century.