On page 258 under the Y-wing weapons it list the proton torpedo as:

Forward mounted Proton torpedo launchers (2) (fire arc forward; damage 8; crit 2; range [short]; breach 6, blast 6, guided 2, limited ammo 8, linked 1, slow-firing 1)

Am I reading this right, it has 4 launchers with a total ammo of 16. If this is right then a player could spend the 1 hard point to link all launches so it has one launcher with link 3

It has two launchers at start, not four. Where did you catch that?

I believe the total ammo is 16 as there are two launchers with Limited Ammo 8, 8x2=16. In that you are correct.

Remember, linked takes the weapons that are linked together and allows an extra hit with the expenditure of two Advantages. With only two launchers, Linked 1 is as close as your going to get.

Now, if a player were to someone add two more launchers by, let's say, removing the Forward Firing Laser Cannons, then yeah, building up the Link rating is possible and brutal.

The Z-95 list the launcher as one with link 1. That is why I highlighted the 2 and link 1 in the OP.

Also the Z-95 ammo is listed as 6, is that total of 6 or 12. )And if the Z-95 is 12 dose that make the Y-wing 32 ammo?)

It is the 2 in the Y-wing stats that has me banging head on the table.

I think the (2) in the Y-Wing may have been a typo as they were denoting how many launchers there were. Others RPGs have done it that way, and that may have just been an error as they were writing things out.

By canon, a Y-Wing has two proton torpedo launchers, and a Z-95 has two concussion missile launchers. Both of these have weapons that are fire linked.

As for the ammo, that part I really can't help you with as there's always debate. As written, I'd say that the Limited Ammo Quality is between both launchers, meaning the Y-Wing has 8 torpedoes while the Z-95 has 6 missiles.

The 8 is confusing. Canon has the Y-Wing holding a total of 8 torpedoes. The weapon is linked, so that means you only should get to fire it 4 times or 8 if you drop the Link 1 and fire them one at a time. To me it almost would have been less confusing to give it Limited Ammo 4 since it's listed as a dual launcher.

Reads pretty clear to me.

You have two tubes, eight torpedos, and you can link the tubes to fire together.

That's four linked shots or eight individual shots.