So, am i right, that when i play a throned throne on a duration i.e. merchant ship, i will get $4 this and next turn, but i cant use the second throne for another card, because he will stay out with merchant ship?
I.e.
Hand is:
Throne Room
Throne Room
Merchant Ship
Copper
Village
Play Throne Room, select Throne Room.
Play that throned throne first time on merchant ship, stays out with it, so it fails to target the village in this turn for its second use?
No; a Throne Room can't "fail to target" the action just because it's already in play. Whether you chose a duration or a non-duration with the first play of the second Throne Room, either way that second Throne Room is in play. And either way you will play it again and choose another action card from your hand to play twice. Nothing in the game would care whether that Throne Room would be discarded at the end of this turn or not; not until you actually get to the cleanup step of this turn.
The specific actions are:
-Play Throne Room A from your hand
--Play Throne Room B from your hand
---Play Merchant Ship from your hand
---Play that same Merchant Ship again while it's already in-play
--Play Throne Room B again while it's already in-play
---Play Village from your hand
---Play that same Village again while it's already in-play
This would all be exactly the same if you replaced Merchant Ship with a non-Duration; or if you replaced Village with another Duration.
Note that the "stays out with it" has nothing at all to do with anything that happens in the action phase; it only affects what happens in this turn's clean-up phase.