That's a really broad topic.

The 'must read' books that spring to mind are Anthony Reid's 'Southeast Asia in the Age of Commerce, 1450-1680. Vol 1: The Lands Below the Winds' (1988) and 'Southeast Asia in the Age of Commerce, 1450–1680. Vol. 2: Expansion and Crisis'. However, those are specific to the time period mentioned so I don't know whether they're what you're looking for.

Your best bet is to check out the book list under Maritime Southeast Asia:

https://www.reddit.com/r/AskHistorians/wiki/books/#wiki_southeast_asia