I maintain WordPress Bengali project and yesterday I pushed the 3.9 translation update from bn.wordpress.org.
You are right, there are no 3.9.x branch there so it’s pretty much not clear to me as well. Here’s how it works: we should always translate from the Dev version. When a new release comes, there is a SVN revision for that WordPress release. We just refer to that revision and build a language pack from the development version (trunk). So whatever it’s there, its been released as the new version.
