In the case of Space X, the trunk section appears to be:
- Structural adaptor between Falcon upper stage and dragon
- Unpressurised storage space for cargo (since falcon is larger than dragon really needs)
- Solar panels
The first seems cheap enough to not try to bring home, the second is possible sub optimal, but comes from the general noodleness of Falcon 9 and the fact that human space craft are low mass per volume.
With the solar panels it would certainly be possible to have either folding panels, or protected in such a way that they can survive re-entry but given solar panels exposed to sunlight and radition degrade and the presence of a structural adaptor trunk anyway putting cheap unprotected panels on it is probably cheaper than engineering and flying a re-usable solution.
As a more general engineering thing, putting re-usable hardware inside a space craft pressure vessel is fine until it needs repair or service, then you can end in a complex morass of 'repair of module X damaged adjacent module Y' as technicians work in the confined space (and only one team can physically fit in there to work at a time). Some hardware may be cheaper to build and expend rather than design for service inside a pressure vessel- an example would be a pump handling (possibly toxic) fluids where doing an all welded 'only has to go in once' design in an open bay may be cheaper through life than a serviceable version with mechanical seals and joints fitting inside the crew cabin.