I bought the upgraded cabin and the pet storage area and installed them in the two slots available on the ship page (under the anchor, etc.). However, there is no difference in the captain's quarters and the pet storage area isnowhere to be seen.

What's the deal with these two items? How do I get them to appear/work? I can't seem to find any information about this.

They work for me, I installed them on several different ship types.

The pets are supposed to be roaming around left of where Eder and Aloth are standing. That too worked for me each time.

Did you install these upgrades in your active ship?

Could this be made to be interactive somehow?
Have some way you can drop your pets in and therefore remove them from your inventory. I still have all my pets cluttering my pack and now also have them all cluttering my boat.
I would prefer them to be doing their business in my boat rather than in my pack.

I only have one ship! The menagerie is now working, but the captain's quarters are still the same as they were at the start. Oh well, nothing really important here.

Have you taken screenshots of your cabin from before and compared it? Maybe the difference is just a really small one on the first ship. All the other ones are... bigger.

What did you do to get the menagerie working, if it didn't at first?

I just realized that all of a sudden there were pets everywhere. But the captain's cabin is stil the same as before. No big deal, just annoying.

Same problem, but I had the menagerie from the start. But was wondering all the time, if the captains quarters changed. It surely does not look like the description praises it ;)