Note that the controls are armored equivalent to cloth, and the heavy machinery equivalent to battle dress. Note also that the sole consequence of a machinery hit is an explosion and potential injury to persons in the vicinity of the explosion. In the Bard Endeavour scenarios, there is no impact on the players' ability to satisfy the scenario requirements (including seizing the bridge to take control of the ship and repairing and starting the jump drives) despite the Solomani player operating under a tight deadline to seize the ship before it falls into a gas giant. It is therefore reasonable to conclude that while specific machinery may be vulnerable, the ship itself contains enough redundancy to continue operation despite loss of specific bits of equipment to stray fire in a firefight.
It would appear then that damage to bulkheads is not an issue and that damage to controls and machinery in the course of a firefight, while dangerous to those nearby, will not affect the ship's ability to maneuver or jump, or at least not an affect that can't be quickly repaired or routed around.