As much as that is RAW (and likely also RAI), what happens with linked missile tubes if you don't spend 2 Advantage to fire the second one?
The 2 Advantage triggers a hit from the second tube. It is fired either way.
But Guided ordinance that misses can still potentially hit on subsequent rounds as long as you can keep paying the Advantage. So where/how do you have to spend the Advantage to get one/the other/both when you factor in Linked as well?
When a weapon with the Linked quality is fired, it represents the entire weapon assembly (including all launchers/tubes/barrels/etc.) firing together. The various missiles/torpedoes/grenades/roungs/slugs/bolts/etc. are all tracked as a single attack*.
*Note that even weapons without Linked function the same way, as a single attack from a Blaster Pistol can still affect multiple enemies (by hitting a Minion Group), friendlies (by triggering one or more Despair while firing into an Engagement), and environmental features (by using Advantages/Threats/Triumphs/Despairs to modify the environment).
This is important to the resolution of weapon qualities. Guided may only be activated when the attack misses, and Linked may only be activated when it hits. So if the attack hits, it ends (Guided may not be activated) even if Linked is not activated.
However, if the attack misses and Guided is activated, the following attacks may still activate Linked if they hit or Guided if they miss (as above), until the attack either hits (with or without activating Linked) or misses without activating Guided.