Is there a way to keep an item from showing in the "Shop All" section?

And it still shows up in other categories? Hmm... probably not. You will need to create a new group of items which has every item in it except the one item you don't want to show, and then use that as a commerce category (replacing the 'shop all' action)

It would be okay if these items didn't show up in other categories. We're using them as add-on charges so no customer will ever shop for them.

Have you tried unticking the Display In Web Site checkbox?

Yea, tried that. The item still goes into the cart (I add it programatically) but doesn't show in the UI.

Sorry, I'm confused. You untick the box, and it still shows up in the Shop All section?

You're correct, unticking the box removes the item from Shop All. However, when I add the item to the cart contents using code, it doesn't show up in the cart UI. It's in the cart contents but doesn't display to the user.

Ah! Interesting.

I'm sorry, I just tested this again. If I uncheck "Display in Webstore" then my order.addItem(...) method fails.

No worries. It's good we cleared that up. So, am I right in understanding that you're trying to add a new shipping cost, and you're using an inventory item for that? Eg, if something is bulky then you want to add an additional cost for that?

I'm using a "Non-inventory Item for Resale", and yes, the rest of your assumptions are correct.