You should definitely combine lightmaps into large atlas. It might help you batch some meshes that use the same materials.And also small wins as you mentioned where the engine won’t have to bind the identical texture and also shader as that’d be the same. Engine also does sorting by many of the mesh / material properties (a sorting key is generated based on these), so you get extra efficiency from this.
But to get the best performance, I would consider putting your other textures on larger atlases. Consider the scenario: You have 100 objects, each has unique smaller diffuse texture, and they share the lightmap. This will end up being 100 render calls (per camera). You could create a diffuse texture atlases, say an atlas could fit 5x5 textures, so 25 in total. If you enable batching in the engine, it could combine all meshes sharing diffuse and lightmap atlases, and you would end up with 4 render calls (this assumes they all use the same material, so other properties need to match too). Disadvantage here is that if you only need 1 objects from a diffuse atlas, you still have to load whole atlas with 25 textures in it. If that is likely scenario, you could give up using compression on that diffuse atlas, and build your atlas at runtime from small textures as you load them.