One would assume that those problems were not apparent or possibly didn't exist on the older warp drives, but became a large problems as they started going faster with higher consumption rates and larger warp cores.
This could be why the refit of the NX-class has a secondary hull, the larger warp core has other issues that the Archer core does not. Or the found the Archer core has long term problems and decided to move the cores to secondary hulls at that time.
However not all ships have secondary hulls. USS Reliant has no such external body for her warp core, and a many late 24th Century ships has been getting rid of or blending the secondary hull into the primary hull.