I'm unsure if this has been reported, I did use Github's search and found no mention of bloom at all, at least not for Majora's Mask 3D.
I am using Citra Nightly #901, although this bug was there even in the Nightly #880 (somewhere around there) version.
Specs may be irrelevant, but I'll post them;
1920x1080 resolution, 60hz monitor.
Nvidia GTX 660 Ti, provided by EVGA.
Intel i7 2600k, not user modified to be overclocked (meaning it is at 3.40ghz and 3.80ghz, not less or above)
So, just like in Dolphin itself with Twilight Princess (GC and Wii), bloom in this game is broken up when you change the Internal Resolution (IR).
I am unsure if Majora's Mask 3D uses other Post-Process such as sun glares, godrays or the like and if those also get broken, again just like in Twilight Princess.
This is a part of Majora's Mask 3D, this one runs at 10x Native Resolution to emphasize on the broken bloom;

Here, same location with almost the same angle (Save for Link's idle animations), at the native resolution;

This one is at the IR I'm using right now, which is Auto (3x or 4x, I suppose?)

By the way, this can actually be easily seen/tested for those who have MM, too. The bloom appears already from the start, you can see "checkerboards" on the trees, as seen here;
Native

10x

Auto

This is a side-effect of the sample locations being stretched up. There is very little you can do here; the game was simply programmed and tested at lower IRs only.
I happens in Pokémon Sun/Moon too. PPSSPP solved this issue with an option called "lower resolution for effects". It upscales everything but some effects, like bloom, that don't cope well with upscaling.
Most helpful comment
This is a side-effect of the sample locations being stretched up. There is very little you can do here; the game was simply programmed and tested at lower IRs only.