I have got a VS2008 database project, and that i produced a publish-deployment script under Scripts > Publish-Deployment, however it seems to become a no-op (even if I put syntax errors in to the file, everything works). The relaxation from the database deployment works though (also it does create my tables). Any clues?

It may sound like you are just placing scripts inside your publish-deployment directory. You really have to include them inside your Script.PostDeployment.sql file. For instance:

:r .\MyScriptName.sql
:r .\MySecondScript.sql

Its not all script within the Publish-Deployment folder just runs automatically actually, just one can. Automatically, it's that Script.PostDeployment.sql file. You are able to change it out if you would like.