They appear in your build menu when in game, click the saved ships icon and they should be somewhere in there.

OK I'll give it a try.

I thought it was a issue of mods not updated for the new version, but i guess i will try it out later too

Workshop ship downloads are not considered "mods" by the game engine.
They are "blueprints" you apply in the build menu.
While in Build, click the disk icon (tooltip = Saved Designs (D)) , then double click "Workshop Ship Designs". There you will find any ships you have subscribe to.

What if the ships are subscribed but don't show under the workshop ships folder?

Then they may not have downloaded yet. Make sure you shut down the game in between, maybe reboot your PC to get everything with Steam to start up fresh again.

You don't need to restart the game. Just go up one level in the in-game file browser, and then go back into workshop ships, and it will be there.

In my experience, Steam does not download items you’ve subscribed to while the game is running. May be a setting, but it’s still something that needs to be considered.

There's a setting in Steam itself that determines whether or not Steam will download while you are in a game. It is turned off by default. Turning it on will allow Steam to download your workshop items while Avorion is running, and you should not need to exit the game to access workshop items. I never do.