Yes, tribes are sovereign, but that doesn't exempt them from the Census. Similarly, it doesn't exempt them from the federal income tax or the military draft. But the Census is basically voluntarily, so there's no coercion. No one's going to force Indians to fill out the forms.
The key point is that it's in the tribes' best interest to be fully counted. Then they can make a better case for funding their economic and social needs. For example, if a tribe is undercounted by 10%, it may get 10% less money for tribal projects.
In short, there's no downside to being counted. Only upside.
But there's some validity to the concern behind your question. Many Natives may be thinking the same thing. E.g., "What's the government doing here? They have no business on my reservation. We're a sovereign nation, so we don't have to do anything they say."
The Census Bureau wants to alleviate such concerns and put Native minds at ease. The question is how best to do this. Hence Tuesday's meeting.
For more on the subject, see 2010 Census Art Competition and The Essential Facts About Indians Today.