PG 271, column 2, weapon upgrades section, Hard Points Required...ummm topic?
See it identifies the difference between a new "weapon" and a new "weapon system" and says "Weapon Systems" composed of more then one "Weapon" only count as a single HP, and not one for each "Weapon."
It seems a little weird at first, especially if you're used to other systems that use HP as the only balancing point. Edge uses Advantage to activate that Linked quality though, generating an extra layer of balance. So it doesn't matter if you've got a System of Laser cannons with Linked 80, if you are only rolling two ability dice you'll be lucky if you can even activate a single link. It'll make a nice light show though...
Now as for the adding an additional weapon to an existing system. I wasn't' sure of this either, until I really read it out. The last row on Table 7-17 (still on page 271) lists the cost of linking weapons. Read it out, it's not the cost modifier of a linked weapons system, it's the cost of actually linking two or more weapons into a single system. So... you have a ship with a single laser cannon and you want it linked, you pay the cost of the second cannon, the cost of the linking, and you have a single weapon system composed of two linked laser cannons. Narratively you might want to say the tech removed the original cannon rejiggered the mounting to make room for the second cannon before reinstalling your original and the new one, replaced the trigger system and firing computer to handle the extra gun, and slapped in some extra capacitors to handle the power needs... but that's what that linking fee was all about.
It's actually kinda interesting as this also allows you to install two independent laser cannons (or take a ship that already has them like say a YT-1300) and link them as an after market option... Good thing to know if you've only got two players.