There's a line in the script indicating that large ships, at least, have "plasma gun defense" turrets. As far as Polaris itself is concerned, it has missiles for offense and its defenses consist mainly of trying not to get hit.
My assumption about the behavior of the landing boat - which is subject to change if an artist comes up with something really appealing that's different - is that, based upon the design and the placement of the thrusters, it's simply a VTOL like the Apollo LM (except, obviously, single-stage and reusable). It would come in presenting the shielded lower surface, extend its legs and land, then lift off the same way. As much as I like to hark back to Forbidden Planet
, the horizontal skimming-along-cruising-to-the-landing-spot behavior of the C57D is not what I have in mind.