From the guidelines in Special Supplement 3 and/or extrapolating from Striker, standard missiles are only fitted with fractional-kiloton "tactical" nuclear warheads which -- especially since they are proximity-detonated, not contact-detonated -- are too low-yield to vaporize most targets.
To knock big ships out with one hit, you need multi-megaton "strategic" warheads, which will be too large and heavy to fit on regular old "standard" missiles.