Just to be 100% sure.
1) A ninja can use 1 ki to make himself invisible as a swift action.
2) So in a round at level 7 he can : Use invisible as a swift action , throw a shuriken at an enemy who is flat footed and gain the 4d6 sneak damage.
My question : At level 8, does the sneak attack goes for both Shuriken ( Because he will have +6/+1 )
This is a slightly conditional issue.
If the enemy is generally aware of you and alert/in combat, the only thing letting you sneak attack them is invisibility. Invisibility will break after your first attack, so the second shuriken won't benefit.
On the other hand, if the enemy is not alert/in combat, for example in the case of you going invisible before they see you/other threats and sneaking up on them, they would be flat-footed. This condition lets you sneak attack them, and remains until they take an action, which means the second shuriken would also deal sneak attack damage.
There's a ninja trick called Flurry of Stars, which lets you throw 2 extra shuriken when making a full-attack (the 2 extra attacks are at full BAB), with a -2 to hit penalty on all of the attacks. It costs 1 ki as a swift action, so if you have time to go invisible in the last round, then Flurry of Stars this round, you can land 4 sneak attacks, or even 5 or 6 if you two-weapon fighting the attack (5 with standard two weapon fighting, 6 with the Improved Two Weapon Fighting feat).
There's also a master trick available from level 10 called Invisible Blade, which treats your invisibility as Greater Invisibility, meaning attacking will no longer break the effect, and you'll benefit from the sneak attack effect on all of your shuriken.
For your second question, I believe you could. That's quite resourceful actually. I can't give an iron-clad yes, but you can 5-foot step during a full-attack action, so I think swifts can likewise be inserted midway.
Also, there is a Rogue Talent, False Attacker, that can help you. When you use False Attacker, you can make a Bluff Check as a Swift Action. If successful, your victim thinks your attack came from somewhere else, and you get to keep Stealth.
The OP's character is level 8. At level 10, his Ninja can take Greater Invisibility as a Ninja Trick, and then he can just fight invisibly.
I've been wanting to do this with a Ninja who dips into Arcanist, using those Ranged Touch Attack Cantrips against Flatfooted AC that also do Sneak Attack Damage. Maybe get a Wand of Scorching Ray.