There is an inconsistency in the design language of the shop that, if addressed, would go a long way to help useability. Some of the menus are organized in rows, and some into columns, while some have little to no organization at all.
First, here are the menus that are organized into rows:
Then, you have Building Blocks, which is organized in columns, and Archery, which is rows for the most part, but has a column to help keep it look nice in the four-wide arrangement:
Finally, you have the menus with no visual organization whatsoever:
In my opinion, most of these can be greatly improved to the benefit of useability if you prioritize rows, for multiple reasons. First, if you organize in rows then any sub-category will be entirely on-screen at any one time. This also helps with future-proofing, in case you would like to add more items in the future. Just to show how this would look, here's the Building Blocks and Miscellaneous menus with this core design decision in mind, as well as some other changes that I will explain:
The first thing that should be noted is that while rows should be used for sets of items, exceptions can be made like in the case of Building Blocks. The three options for buying each material are enough; adding a fourth would make the menu bloated with too many ways to buy the same exact item. With the empty space to the right you can place the special building materials, taking a little inspiration for how the archery menu is handled (I love the Archery menu, by the way. Don't change the layout). However, this column is on the right (as opposed to on the left, like the Archery menu) because the player is less likely to want those materials. In the same vein, Obsidian is much more important and likely to be used, so it should be in sight as soon as the menu is opened, no scrolling required. In my experience, very few people use haybales even though they are above obsidian in the current non-beta UI, so they can be put in a place that requires the player to scroll down a little.
Now let's cover the changes to the Miscellaneous menu. First, the ladder does not belong in this menu, as this is not where people would look if they were trying to find ladders, so it has been moved to the Building Blocks menu (conveniently making that menu more filled out and nice-looking). Second, categories are prioritized over price. The top row is utility items, with chests together on the right because they aren't used as frequently as pearls and tracker compasses. Next, items specifically designed for attack are in the second row, ordered from least expensive to most expensive. Finally, special movement items that require emeralds to purchase have their own row. You can organize this menu in a couple of different ways (I actually went through a few versions before settling on this one), just make sure that the items are grouped in a way that makes sense based on how the player will use them.
The worst-looking menus also happen to be the hardest to fix. Namely, the Weapons and Tools categories. These menus are sparse, so it's not easy to improve them individually. This gets harder when you consider that Hardcore mode takes some of these away (or possibly keeps the slots but locks them, if you implement my suggestion from the section on the Armor menu). In situations like this, ideas that seem crazy at first can turn out to be just what you need. Case in point, here's a picture of both the Weapons and Tools menus combined:
Note that one of the diamond pickaxes is gone because you really don't need five different types of diamond pickaxes. I'm not sure which one would be the best to remove, but I do know that one of them can be removed. This layout has the added benefit of having a column available for adding future tools and weapons (possibly things like fishing rod, axe, and knockback stick).
In my opinion, Archery and Food are perfect as they are, though you might consider getting rid of the Power V bow in normal mode.