The messages are keeped in memory even deleted

The memory on my iphone is full, i have 4.6GB of Message. SO i go in the messages app to delete all of them but even if I delete the message in the Messages app when i go in Settings/General/Usage I see that the memory used by message hasn't decreased.

When you delete a message it is 'marked as deleted' and disappears from the the Inbox and reappears in the 'Deleted' folder. However, in reality, it is still in the Inbox, just not displaying as it is 'marked as deleted'. So, if you deleted in error it is easy to get it back.
Compacting will remove all traces of the 'marked as deleted' email.
Read more info on compacting - what it does and why it is important:
* http://kb.mozillazine.org/Compacting_folders
What you are describing sounds like you have not been maintaining the folder by regular compacting. So the folder is showing some signs of corruption.
As the folder may be corrupted, before you do anything, move all emails into a suitable folder. When you have moved everything you want to keep, delete all other emails and then right click on folder and select 'compact'.
It is advised that the Inbox is used as an Inbox for incoming emails and not as a general storage for mail. see info at link below.
Advise on how to maintain a healthy Thunderbird:
* http://kb.mozillazine.org/Keep_it_working_-_Thunderbird

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