In the introduction to the Vilna Edition of the Ein Yaakov by publishers, a short history of the printing of the Talmud is given (this is perhaps the source for Marcus Jastrow's speech, below).
On this page, in the middle of the second column, it gives a reason why the word Talmud was censored from inside of the Gemara, even when the word is not actually referring to the Gemara, but rather to learning.
This started with the Basle edition of the Talmud. The Basle edition of the Talmud was printed under heavy censorship (see here). Because it was forbidden to call the Talmud by name, a zealous censor took it upon himself to change any mention of the Talmud to "Shas" or Gemara".
Other reprints copied this, not realizing it was a result of censorship.
This is discussed at length in the Sefer Dikdukei Sofrim, Megilla, where it talks about the printing of the Talmud.
Marcus Jastrow, in a speech titled THE HISTORY AND THE FUTURE
OF THE TALMUDIC TEXT - A LECTURE DELIVERED BEFORE THE GRATZ COLLEGE OF PHILADELPHIA - December 9, 1895 said as follows:
" Pope Gregory IX, in 1239, decreed the cremation of
the Talmud, and hundreds and thousands of copies were
burnt in France and Italy. In 1264, Pope Clement IV
set the penalty of death on whatsoever person should
harbor a copy of the Talmud in his house."
The printing of the Talmud began as early as 1494 in
Soncino. The luckless book was still under the ban of
the papal and imperial interdicts, and even when, thanks
to the untiring efforts of influential Jews and Christians,
fortified by offers of bribes more or less open and direct,
permission to print was granted (by Pope Leo X, in 1520),
it was so guarded and restricted as to make a complete
and accurate edition an impossibility.
That the permission granted by Leo X did not secure
immunity from persecution, we learn from the fact men-
tioned before, that autos-da-fe, were renewed at intervals
from 1533 to 1599. In fact, when, in 1564, at the
Council of Trent, the Italian Jews petitioned for
permission to republish the Talmud, the license granted
was, in spite of a vast amount of Jewish money in the
pockets of the Bishops, still more restrictive. Even the
title Talmud was to be omitted. We do not find, how-
ever, that the Italian printing houses availed themselves
of this dubious mercy.