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Codex seems to say for each group of 5 Termies, you can take one Cyclone Missile launcher OR one heavy weapon, but the assembly instructions with the models say one of the options is to have a squad containing BOTH a Cyclone Missile Launcher and a heavy weapon.

What's the answer here? Is there an update to the Codex that I haven't been able to find, are the model instructions just wrong, or am I reading the Codex incorrectly?

The model instructions have no bearing on the game at all. It's hard to even call them "wrong" per se - they just show you how to put together each type of model. There is no reason to believe that the instructions will give you a legal squad. I doubt most players even read the instructions (I know I only ever pull them out when I find a bit or piece that I don't recognize).

As for why they have the instructions written that way, it's probably because they haven't been updated for years and back in 3rd or 4th edition, Terminators could have 2 special weapons per 5 man squad.

It could simply be an example on how to build both type of heavy weapons.
What matters are the rules in the codex.

 B0B MaRlEy wrote:
It could simply be an example on how to build both type of heavy weapons..

This. The instructions have to show you how to assemble everything. That's what they're for.