You’re looking at it only from the perspective of researching the history and with that approach, you are right that the Haida are quite insignificant. Their population was tiny and they only controlled a few islands so on the surface they don’t seem like a strong contender for a civilization. However, I think there are many compelling reasons for their inclusion. The two primary reasons are the representation of the peoples of the Pacific Northwest (who as a whole are significant), and the many features of the culture that would translate into gameplay.
Haida would be a good representative of many of the cultural elements shared among the peoples of the Pacific Northwest. Things like Potlatch, totem poles, dugout canoes, matrilineal kinship, longhouses, slave raiding, etc. These cultural elements have some of the greatest intensity among the Haida. Their art is beautiful and iconic, they raided nearly the entirety of the west coast, and their warlike culture is a perfect fit for a game about just that. There’s just so much that could translate to units and gameplay elements.
They had enormous canoes that they use for their raids and to clash with Europeans. They even captured some of their ships and artillery. A robust navy (not in a gimmicky way) and plausible artillery is something most of the other contenders for native civs lack. They could even introduce new mechanics like this:
They built hilltop fortifications, longhouses, and totem poles so they could have strong buildings with some unique options for the function of totem poles.
Their land military also has decent options with weapons like knives, bows and arrows, firearms, and units with wooden armour like this:
The only thing they’d be missing is cavalry. Living on heavily forested islands with easy transportation via canoe makes horses not very useful to them. A shock infantry unit like Aztecs and Inca would probably be enough to fill that one gap in their roster.
Zulus and Xhosa are in the far south of Africa. The Shona are actually pretty far away in Zimbabwe, Zambia, and northern Mozambique.
Indonesians and Malays are quite distinct, I think you may just be getting confused by the term “Malay Archipelago”. There is a Malaysian ethnicity, but there isn’t really an Indonesian ethnicity. Each island has many different people groups that can be extremely different. This map shows the massive amount of diversity.
https://upload.wikimedia.org/wikipedia/commons/8/8f/Indonesia_Ethnic_Groups_Map_English.svg
This map can be a little misleading since the island of Java makes up 55% of the population of Indonesia and Javanese alone make up 42% of the population. The Javanese also have the heritage of the Majapahit Empire which ruled most of Indonesia before collapsing shortly before the game’s timeframe. They’re twice as numerous as Malaysians and clearly distinct so I think they could both be included as civilizations in their own right.
You can see that Malay occupy the coasts of Sumatra and Borneo (as well as the Malaysian peninsula) and are obviously the most widespread. I think that, along with their history is enough to earn them a place in the game. I made a post about them being a minor faction, but they could also be reasonable for a full civ.