Making assessinations in several system has had the effect that my Reputation with Federation is -100% and my PMF is also in the Federation.
Has this any impact in my actions for my PMF?
Superpower rep affords a
direct raw multiplier on reputation changes with aligned factions. Big emphasis on "raw" and "change"; this means it doesn't work in the way you think it might. A quick little table, where I've made the numbers up, but it's not an unreasonable assumption based on my observations:
Hostile Superpower Rep = 1/4 x effect
Unfriendly Superpower Rep = 1/2 x effect
Neutral Superpower Rep = Standard effect
Cordial Superpower Rep = 2 x effect
Friendly Superpower Rep = 3 x effect
Allied Superpower Rep = 4 x effect
What this means is, if you're allied to, say, the Empire... rep gains will be 4 times larger with any aligned faction, but equally, any rep loss will be 4 times larger too.
Meanwhile, if you're Hostile to the Empire, rep gains will be 4 times smaller, but rep losses will also be 4 times smaller.
That's the only effect; i.e being allied to the superpower doesn't affect influence gains or rewards.
One additional question. In the Navigation Beacon in one system, I see many agents of powerplay. If I kill these ships, is some affected?
I mean, this would affect to the controlling Faction? To the Powerplay? To none?
If you destroy those ships, and it's a crime, you'll hurt the influence of the controlling faction unless they're an Anarchy (violent crimes hurt influence in that jurisdiction)