Disclaimer: I'm not a modding guru so this is more of a layman's Public Service Announcement. I'll use a few technical terms (which may be the wrong ones), but hopefully this will help shed some light on an on-going issue for people using crafting mods.
TL;DR: Don't use a lot of big crafting mods.
If any of you are like me and like to build massive settlements and have the ability to craft everything imaginable, then you've run into a frustrating problem. Fallout 4 has a limit when it comes to crafting menus and objects. This includes both settlement workshop menus as well as crafting station menus. Depending on who you ask the general opinion is that too many keywords and categories cause mod conflicts that flat out limit how many crafting mods you can use without issue. That issue being: missing objects, missing menus, category name overwrites, and probably a few others I haven't experienced.
Various fixes have been made and proposed, but like all Bethesda games your load order is a big factor. Until we get the GECK or someone manages to stumble on what exactly is the cause of the limit, we all basically have a choice: prioritize which crafting mods you want the most and stop adding more once you hit the "limit" and you start missing objects.
I'd like to share a basic load order for, strictly, my crafting mods to give an example. I've highlight settlement specific mods in orange, item-crafting specific mods in cyan, and combination mods in green. (I apologize if these colors don't show properly on your screen).
Homemaker - Unlocked Institute Objects.esp
Craftable Armor Size.esp
Crafting Workbenches - Ammo.esp
Crafting Workbenches - Ammo Special.esp
Crafting Workbenches - Power Armor.esp
Crafting Workbenches - Pre War and Manufactured.esp
Armorsmith Elianora Extended.esp
Using this current setup with this load order results in my settlement building menus to be flawless. No missing menus, no missing objects. I do, however, have item-crafting menu glitches were some categories are overwritten by another mod (I find this annoying, but not game breaking in any way since all the objects I want to craft are still there).
Most every mod in this list is at its current release version as of the moment I'm writing this, and different versions can change results drastically. Just as drastically as incorrect installation procedures (ALWAYS, ALWAYS READ INSTALLATION INSTRUCTIONS!)
My hope is that this issue is resolved sooner than later, but until then I hope this post can shed some light for people new to modding, or just don't know why their mods are "broken."
Best of luck to everyone out there and a big thanks to all the modders who make games more enjoyable for the rest of us!