We have treaties and agreements with Germany and NATO for those bases. There is no authority in those treaties that would allow our military forces to seize assets from a civilian company there.
SO if we break the treaty rules, what’s Germany gonna do? Invade USA? Without enforcing powers rules are not worth the paper they are written on. All our judges have power because we have very strong armed law enforcement to enforce their rulings.
In this particular case is it possible that criminal evidence was presented to Germany and the server was asked to be extradited? That would be far easier on German pride than a German citizen grabbed by US military. After all it was just a little machine owned by a non-German firm.