To reproduce:

1. Download and open attached "repro926832.zip" project.
2. Open Lighting window.
3. Generate Lighting.
4. Go to Project->Assets->Main folder and notice generated lightmaps.

Expected result: Only necessary lightmaps are created. Lightmaps from scenes without lighting do not take up a lot of space or are not created at all.
Actual result: Unnecessary lightmaps are created. They are empty but they are the same size as normal (not empty) lightmaps.

Reproduced with: 2017.2.0b2, 2017.1.0f3, 5.6.2p3, 5.5.4p1.

Notes: This always happens no matter how intense the light is. Ideal situation would be that if the light does not affect other additively loaded scenes, lightmaps for that scene are not generated or are generated but way smaller.