Hōkūleʻa should not fly the USA flag, nor fly it above the Hawaiian Kingdom flag.
Double-hulled canoes came to the Hawaiian Islands from Polynesia, not from the United States of America (USA). There is also no treaty of annexation which ever transferred Hawaiian sovereignty to the USA. The government of the Hawaiian Kingdom was illegally overthrown in 1893, but that did not extinguish its sovereignty and independence as a nation-state. The Hawaiian Kingdom became the first non-European member of the Family of Nations in 1843. The continuity of its sovereignty and independence as a state, and subject of international law, has been presumed ever since. Without a treaty of annexation, the USA flag should not be flown on the Hōkūleʻa, much less flown above the Hawaiian Kingdom flag.
The USA flag is unabashedly flown above the Hawaiian Kingdom flag on the Hōkūleʻa in this recent video: vimeo.com/140853625