I am quite sure, that pathfinding is the issue for most settlement builders.
The other things mentioned here may be also true, but pathfinding is (and ever was) a major issue in this engine. I remember things Beth said with the Oblivion builder set, and with FO3 too, as far as I remember. If you built inside cells (interiors), it was not a big issue. But everything outside had to integrate into the worlds pathways, or it would make troubles. There was an extra function in the editor, but very hard to use without experience. Essentially they had overlayed the normal ground with walkways (invisible in game of course) so that the NPCs could travel along.
I think the settlement objects have all this ways integrated, but only if you let them snap together. If you place them manually it can lead to an impassable or hard to pass place. Sometimes you see it, sometimes it will not be obvious. I had a guard station badly build - the stairs were too high above the actual ground. The assigned settler was assigned to the station and it highlighted when I selected the settler. But he kept standing around. When I corrected the problem he immediately started to walk to the station and guards it since then.
But being unable to find a bed, or unable to walk their normal routines, whatever they are is not so clear. Settlers who are unassigned walk around too, they go to the bar (if any) in daytime, and so on. Theoretically should every settler without a job automatically collect scrap, i.e. also have a job. This should happen even without a scrap bench. So settlers who are standing around too long in one place are suspicious - something happened to their path. There seem to be several path finding algorithms in the game, good ones, which have strategies to go around obstacles and others which are less strict and cost less CPU cycles. All the settlers and most other NPCs, if not moving during quests seem to be unable to go around obstacles. Often you see settlers walk into a wall and hanging. If a cell is not loaded, this is much easier, there is a relaxed mode who always works, but there is no NPC in an unloaded cell, it is only his location which is moved around. And schedules (which move NPCs, make them go to bed, and so on) do not run in an unloaded cell at all. If you have many settlers and fast travel directly into the settlement, you see all the NPCs spawned in the center. They begin to start their schedules, but they also hinder themselves and the path walking seems to be suspended, if mo easy path can be found. Maybe this leads to wrong assumptions by the settlement scripts, and to falling happiness.
I understand the problems with path finding, since I know how it works. To find paths for say 20 settlers is not simple, and will become a load on the engine, if you have added a lot of additional walkways by building a lot of things. The path finder must check every walk path around the settler to his target, and this can become quite big, even for todays engines.
I hope Beth is able to correct a bit of this by modifying the scripts. I they even try...
Luckily I am not really interested in achievements, so if happiness is around 80 I am content. But being unable to reach one achievement is a good argument to do something. Probably just by making it easier