It's an interesting question.
From my point of veiw, the open doors don't count as part of the drop pod. Can't, if you want to be able to actually put a marine standing on them. It's like unloading and leaving guys standing on top of a landraider.
We've generally played it as you measure from the hull of the pod itself for deployment. Open doors count as terrain for moving over (except running straight down them of course), and can give some cover to infantry iff they actually block part of the los to the model. Tanks and enemy infantry can move over the doors, with only the pod counting as a model.
So from that perspective, how the marines unload and deploy from the pod, and how you deploy the pod on the table, isn't changed at all by having it closed. What does change is LOS through the middle of the pod.
So if an opponent would like to claim he can target through the pod, I'd let him count it as open. At that point I don't think there should be a problem.
Most of the guys up here leave them open but with minimal painting on the inside. Spray of AP metallic, and badab black wash before putting them together.