Great question — answering as the UphillTech team:
It's not reasoned anywhere within the MCU, or outside of it to my knowledge but if we look at how it's used in the films: Out of Universe: it was a nice nod to those who knew or bothered to work out the acronym in Iron Man, and those that didn't get a nice intro at the end, S.H.I.E.L.D. is a major part of Marvel's comics. and using it's full name was a way to reward the knowing audience without removing anything from the unknowning In Universe: as Dave linked in the comments above to Horuskol speculative answer here the full name is given to civilians, whereas government groups are given the abbreviated name S.H.I.E.L.D. After that in the films S.H.I.E.L.D. is used always, but no civilians...
Full answer by Blade Wraith: https://movies.stackexchange.com/a/97688 (CC BY-SA 4.0).
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