This passuk is the subject of a famous difference of opinion between Shimon (or Nechemiah) Ha'Amsoni and Rebbi Akiva. This is in several places in Shas, and the first in Kiddushin 57a.
Reading the Gemara immediately elicits some obvious and important questions. What did Reb Akiva know that Reb Yishmael did not? Or, alternatively, what is the machlokes between Reb Yishmael and Reb Akiva? And more interesting, what did Reb Yishmael do with the many, many instances prior to this passuk that use the word "Es" with Hashem's name? In fact, right in our parsha, eleven psukim before, the passuk says לְמַעַן תִּירָא אֶת ה' אֱלֹקיךָ. What did he do with that "Es" that he couldn't do with this one?
Rabbi Shain, a Rebbi in Yeshiva of Staten Island, in his excellent sefer "Birkas Ish" (in Parshas Miketz), shows us a clear answer to this question that ironically answers nothing at all.
We find, he says, that Onkelos translates אֶת in several ways. In Breishis 37:2 by הָיָה רֹעֶה אֶת אֶחָיו בַּצֹּאן, וְהוּא נַעַר אֶת בְּנֵי בִלְהָה וְאֶת בְּנֵי זִלְפָּה he translates both Eses to mean עם, with. In Shemos 9:29, he translates ויאמר אליו משה כצאתי את העיר as from/מן. Of course, most of the time Onkelos translates את as ית. It is clear that when את has a function in the passuk, Reb Yishmael doesn't darshen it as a ribui at all. It is only the את that means ית that Reb Yishmael darshens as a ribui.
In the context of Hashem's name, he notes that in Breishis 44:18, Yosef said to his brothers .אֶת הָאֱלֹקים אֲנִי יָרֵא; In Shemos 1:17 it says וַתִּירֶאןָ הַמְיַלְּדֹת אֶת הָאֱלֹקים; and in Shemos 14:31 it says וַיִּירְאוּ הָעָם אֶת . Examining these cases, we find that in every iteration of "את השם", Onkelos translates it either as מן קדם השם or קדם השם. The first and last time that Onkelos translates it differently is "את השם", where he translates it to mean ית השם.
So this definitely answers the question. It is only את that means ית that Reb Yishmael darshens as a ribui. Even the קדם and מן קדם have a function in pshat in the passuk. The one and only time that את means ית in the context of Hashem's name is our passuk, which Reb Yishmael would have had to darshen as a ribui.
The question remains, what is the difference in this passuk from every other similar passuk that made Onkelos translate it to mean ית and not מן קדם or קדם.
Reb Yonah Valler, in his Kanfei Yona in this week's parsha, says that he understands the Machlokes between Reb Akiva and שמעון העמסוני as similar to the machlokes between the Rambam and the Geonim on chatzitza of hair. We mentioned above that from the words ורחץ את כל בשרו we learn that when you go to the mikva, you are required to be tovel your hair as well as the rest of your body. Thus, dirt or knots in the hair that prevent contact with the water raise a Chatzitza issue.
Generally, the rule of Chatzitza is that רובו ומקפיד, something that covers a majority of the object, and the person doesn't want it there, it is a chatzitza mid'oraysa. How do we define majority of the surface of a person? The Rambam holds that we add the surface area of the hair to that of the body, and a majority of that sum is called a majority. The Geonim hold that the hair is viewed separately, and if a majority of the hair is covered, even though it's a tiny minority of hair plus body, it is a chatzitza de'oraysa. (We pasken like the Geonim.)
The Ran in the Rif's hilchos Niddah explains the machlokes like this:
The Geonim hold that since we darshen Es to mean hair, it's like two pesukim: an explicit passuk for "body" and an implicit one for "hair". Therefore they hold that if the majority of the hair is covered, it's a chatzitza. The Rambam holds that even after the drasha, all we know is that the hair is counted as appurtenant to the body, so we add the surface of both to determine if the chatzitza covers a majority.
Thus, he says, if you say like the Rambam that the Ribui of Es to add another implicit but coequal and equivalent element, there's no way that we can include talmidei chachamim in our passuk. Talmidei Chachamim are not coequal with the Ribono shel Olam. This is the shitta of שמעון העמסוני. If, however, you say like the Geonim, that the ribui of Es only says that along with A you have to also consider B, then there's nothing wrong with saying that Es by Hashem includes Talmidei Chachamim. This is the shitta of Reb Akiva.
He adds that this explains why the Rambam in Shoresh II in Mitzvos brings that the Bahag holds that the fear of Talmidei Chachamim is counted as a mitzva separate from fear of Hashem. The Rambam argues and says that it is appurtenant, not coequal. This, of course, is the Rambam leshitaso by tevilla of hair. Es is only appurtenant, not coequal.
So now, let's get back to our question. שמעון העמסוני knew of our passuk when he started darshening the word Es back in Breishis, and it apparently never bothered him. What changed? There can only be two explanations: That he used to think it meant מן קדם, so you don't have to darshen it as a ribui at all, or that he always knew it meant ית and that it was a ribui, but he used to hold like Reb Akiva that it means appurtenant, not coequal.
(just to get this Yetzer Hara out of the way, I need to mention that in Yeshivos, they say pshat in Reb Akiva's chiddush of לרבות תלמידי חכמים is that even a Talmid Chacham needs to be a Yarei Shamayim.)