To start, I'm glad that your ship inventory follows you when you switch home ships. It would be a pain to have to transfer everything manually and end up with multiple ships housing forgotten inventory forcing you to search ship after ship in your fleet to find specific items. However, my primary ship is built out to have an armory with cool things I've found displayed in weapon cases, on racks, etc. When you switch your home-ship, everything is dumped in to main inventory on the new ship, and even if you switch back to your original ship, the items are again dumped in to the main inventory. Not only does this hamstring the coolness of being able to display gear on a ship, but it can screw you over if the display items put your total inventory overweight in main storage. Over the course of certain questlines, you need to switch ships for the story, or maybe you come across a ship you decide to "liberate", or maybe it's a ship is a quest reward, regardless, your inventories get jumbled up. It seems to me, that your items could be tagged by the game to indicate which storage they were in (main, captain's, other, display) so that as they move from ship to ship they can be better located. Additionally, I think the game could save the state of your inventory items and when they go back to a ship you've already set up, they would default to where they were before. I guess we'll have to see what the modders can do.

TLDR: Why would I take the time to display my items if it's all going to get thrown in to main storage anytime I switch ships..?