It's a much more difficult problem to build a museum addressing the Native exterminations and massacres that occurred than one focused on the Holocaust. The Holocaust was specifically targeted in both time, extent, goals, and oppression. While you can discuss precisely when it began, it certainly didn't happen until the mid-1930s and ended around the same time as the German surrender. The genocidal policies of the Nazis were clearly directed towards the extermination of 'unfit' groups and we see a very clear documentary trail of buildup by the centralized Nazi regime.

Compare this to Native colonization, where we're talking about no less than seven different governments (French, Spanish, English, Dutch, Mexican, and American) over a period of centuries. Within each of these governments were a number of evolving policies and groups that took different approaches to both natives as a whole and each particular subset thereof. This alone would be a huge undertaking, but we can't even stop at the policy level. Local authorities and actors played tremendous roles in shaping broader interactions, interpersonal conflicts and small events at times spiraling into generations of warfare and killing. One of the key characteristics of American 'frontier' policy was a lack of centralized control over westward expansion. Policies in the far west often remained intentionally outside federal oversight and attempting to address the complex nature of political control while properly discussing genocide is much more difficult as compared to the hyper-centralized Nazi regime.

None of this is to say that people haven't attempted to address the issues. The AIGM has confronted them in a rather unsubtle way. The NMAI has also attempted to address genocide and exterminations, but rather more subtly. Ironically, the latter's choice of highlighting native voices and commentary tends to suppress discussion of the most egregious atrocities, for which there were few survivors with descendants the Smithsonian could attempt to contact.