I just last week up loaded an updated mobi to them. I have only uploaded mobi's for the past couple years. So IMO they must accept them.
Their DOC->MOBI creation stinks, IMO, so I am glad they accept mobi. I build the EPUB and MOBI in Scrivener. Scrivener uses Amazon's tool to create the mobi and it produces a much nicer file then their online tool.