Seems like a mods compatibility issue, either conflicting with another mod that makes changes in that specific interior map, or simply conflicting (glitching) the default game assets of that location. I doubt that there would simply be completely missing meshes in the default non-modded game, but nothing is impossible when it comes to Bethesda game bugs. Maybe it's just related to data not loading properly there following a fast travel (regardless of mods).
It's going to take some time (I.E. a lot) at figuring out what's causing the problem, lest you remove mods one by one and try your saved game again every time. Additionally, if you save the game with dozens of mods installed, and then remove a number of them... at some point or another you just won't be able to load your game anyway since it relies on data coming from mods that just won't be there anymore (which won't even be related to your original issue). It depends on the types of mods you have as well of course.
To start your investigation I would recommend that you simply make 100% sure that you don't have a single mod that modifies anything to the Nipton Town Hall to start with. Check each one of those mods' respective pages over at Nexus (or wherever you downloaded them) and see if they mention anything about the town hall specifically. If you do find even just one mod that happened to change something inside it (texture, model / mesh / script / quest, really anything) then start by removing that one mod and see if your game can be loaded again to start with (and if it does and the issue is gone, then you'd know right away). A bad (time consuming) scenario would be that there's one (or more) mod that modifies certain types of files that happen to be inside the Town Hall as well, without necessarily being made to intentionally modify the Town Hall per se. For example, a mod that would modify meshes for higher quality (polygon count) in the game's assets for the whole game map, and every one of those meshes are modified. So under that circumstance you'd have to remove all such mods just because the Town Hall happens to contain the type of files affected by said mods (and removing mods that way one by one is really bad for anyone's sanity).
I used to mod for Fallout 3, and I think I've done more elimination process troubleshooting than I've done any actual gameplay (and I had a blast at it nonetheless). If you're lucky enough, you'll find out which mod is the culprit right away and it's just gonna take five minutes to fix the issue. If you have to go through your 40 mods or so... then I hope you have patience.
Good luck.
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