Imagine the difficulties decommissioning a warp core and related assembly.
However, removing the actual reactor is a trivial exercise. In fact, that's a standard emergency measure. All you need to do is place a glass tube with an electroplasma inside for the proper lightshow and a speaker system for the sound and you can recommission an 'active' engineering bay in a museum ship that's safe to operate.
Can't exactly do that with a nuclear reactor build straight into the ship and meant to not ever be removed.