@AndreJ showed us the way.
First you have to know that when adding a Layer
from your database, the database parameters are burnt into the QGIS project file.
This mean if you modify those parameters from QGIS source, it will not affect you project file.
If you need to modify those parameters there is only 2 solutions :
1/ Remove the layer and re-import it with correct parameters.
2/ Editing your QGIS project file with a Text Editor (our case because was many styles and scripts in the layers) and find those lines :
<datasource>dbname='MyDatabase' host=localhost port=5432 user='MyLog' password='MyPass'... </datasource>
and add estimatedmetadata=true
in order to activate estimated table metadata option :
<datasource>dbname='MyDatabase' host=localhost port=5432 user='MyLog' password='MyPass' ... estimatedmetadata=true ... </datasource>
We can now open our project in few seconds instead of 10 minutes.