I\'m designing a realtime strategy wargame where the AI will be responsible for controlling a large number of units (possibly 1000+) on a large hexagonal map.
A unit has
This question is huge in scope. You are basically asking how to write a strategy game.
There are tons of books and online articles for this stuff. I strongly recommend the Game Programming Wisdom series and AI Game Programming Wisdom series. In particular, Section 6 of the first volume of AI Game Programming Wisdom covers general architecture, Section 7 covers decision-making architectures, and Section 8 covers architectures for specific genres (8.2 does the RTS genre).