I just learned this term yesterday. The name reveals itself. It looks like you can build molecules, complexes or even metal clusters in zeolites or nanostructures(?) and then trap them there. Really interesting. I have always liked "ship-in-a-bottle" things. By the way, I made a quick search on ACS using both "ship-in-a-bottle" and "ship-in-bottle," a total number of 9 publications were found. So, it might not be used so frequently. Or may be it is a really difficult technique just like building a ship in a bottle.
image is from : “Ship-in-Bottle“ Catalyst Technology by Masaru lchikawa. If you google it, you can download the pdf for free.