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In the Imperial Armour Aeronautica book, the Hyperios battery missiles have "Heat Seeker" but the platform itself is already listed as being twin-linked. Is this just some bad copy-pasting, or does this unit somehow magically bypass the "re-roll a re-roll" rule?

Lol, it's bad copy pasting.

Or for fluff reasons - I can see my friends LOLing because it isn't heat seeking if the rule was absent.

Not bad copy and pasting at all.
True the Twin-Linking does make the rule redundant, but not all vehicles have a Twin-Linked version.
It's simple the rules of the weapon.

6th edition does still have the "never re-roll a re-roll" clause right? I don't have my book handy.

Yes it does.