Page 11 of Starships seems to indicate that, yes, you base a sub-ship's reliability solely on that sub-ship's equipment (2nd Paragraph of "Effects" section of Multivector Assault Mode, where it says each sub-ship receives its own damage and shield tracks).
The fourth and last paragraph of the "Effects" section of Multivector Assault Mode expressly indicates that, when the separated sub-ships rejoin the main ship, you subtract the sum of structural damage of the individual sub-ships from the main ship's structure, and apply the resulting effects normally.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz