I understand that there are some items used for food, and some items used for construction, and then items with special uses (for example, the rainbow jar)-- but what is the purpose of items such as cuttlefish ink, shells, hops, laminaria, and soapshroom?  

I haven't found anything they're good for thus far....

You listed pretty much all the purposes of items already. All the items you listed are used in building. Ink is needed for the Cartographer's guild, Shell for Carpet and Mantle, which in turn are needed for Embassy and Townhall lvl 4 respectively). Hops and Soapshroom are for the Inn and Laminaria for bandages.

You can see a list of buildings / items and how to build them here: http://beastkeeper.com/recipes-list (Help -> List of Recipes)

Ah.  Thank you, ma'am!  I was curious about whether or not I should keep all the items in my inventory.  I suppose that answers that!