Constructors get destroyed upon construction of a starbase module because they use nanotechnology to convert the mass from the Constructor ship to the mass of the starbase module and their crew mans the module.
Colony Ships inevitably get destroyed because of atmospheric entrance, and in order to set up the Initial Colony building.
Freighters probably don't get destroyed at all: they get dismantled and converted into those tiny trade ships.
There may be several reasons why Transports get destroyed:
1. Atmospheric entrance under fire.
2. They get destroyed on the ground.
3. Their mass, like in Constructors, get converted by a nanotech device, into the mass that forms those hideous lunch box tanks.
4. They are dismantled once the ground war is over.
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A Spore Ship may get destroyed because of:
1. Atmospheric entrance under fire.
2. Self-intoxication from releasing spores.
3. Kamikaze(crashing into planet to release spores into soil/oceans).