Probably not? It strikes me as a little weird, but only for the combined reasons of:
a) this might be a personal misunderstanding, but S.H.I.E.L.D. always struck me as at least partially covert, so their insistence on branding makes me laugh
b) the Helicarrier has retroreflective disguise tech, which tells me that at least in part it's meant as a stealth tool
c) even ignoring the previous two points, assuming they want the logo on there somewhere in case they need an easy source of visual identification, on top of the turbines seems weird to me, because that would only be visible to anyone above them and it seems relatively small.
All of these reasons might be completely off-base, I just noticed it during the launch scene and thought it was funny. XD
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