The Logistics one will work if you connect the planet with the Logistics building to the shipyard you are building the ship you want the bonus to apply to.
Bit of a nasty sentence there but you get the picture.
Even if the H.L. planet is giving the shipyard just one building point then the H.L. bonus will still apply.
This way you can move your 'magic' shipyard to the front line just by connecting it to the H.L. planet.
