Saganami-C vs a pre-war superdreadnought
1) In general, could a single Saganami-C defeat an old-style superdreadnought, circa 1905pd?
The answer, assuming that the old-style superdreadnought has circa 1905 electronics and defensive systems, is probably yes. And (allowing for your final question under #3, below) adding the additional proviso that a mission kill could undoubtedly be scored more quickly than the total destruction of the target.
2) How much fire control does a Saganami-C have, and is it sufficient to control enough missiles to batter down a SD's defenses? The argument has been made that because of the fire control upgrades made under the Ghost Rider program, a CA now has the control ability to handle at least a couple hundred missiles at once. The idea is that a Saganami-C class could dump 5 or 6 salvos out of the tubes with delayed timer settings, and thus fire off a couple hundred missiles without ever using a pod.
The limiting factor on a Saganami-C in this sort of engagement of is more likely to be magazine capacity rather than fire control. It takes a lot of hits to kill a superdreadnought, and although I don't have the figures right here in front of me at the moment, the total loadout for a Saganami-C is on the order of 1,000 to 1,500 missiles. That includes all of her electronic warfare platforms, as well as laser heads. And, although the new missiles have heavier warheads than old-style cruiser missiles, they still don't have heads as heavy as those mounted by "proper" capital ships circa 1905. So it's going to take a greater number of hits to destroy a superdreadnought, even if it's a bit elderly, than would be the case for another superdreadnought. The Saganami-C would be able to handle substantially outsized salvos, but I'm not sure it could handle five or six of them. However, see my response to your final numbered point, below. Against outdated defenses, that wouldn't be the controlling factor, simply because the improved EW and penetration aids available to the Saganami-C would more than offset the smaller salvo size.
3) Is the effectiveness of Ghost Rider ECM enough to offset the heavier, more effective defense systems of a SD, assuming that the Saganami-C ship is only firing 40-missile salvos? And is that offset enough to generate a kill as opposed to inflicting minor to moderate damage?
In general, the answer is yes, again assuming that the superdreadnought's electronics and defensive systems are also circa 1905. Against an "old-style" superdreadnought with updated electronics, the Ghost Rider advantage would decline sharply. The cruiser would still be able to get hits through, even against the new  defensive systems, but not in the concentrated numbers necessary to kill or cripple a superdreadnought. A "golden BB" would always be a possibility, of course, and depending on where the combat was taking place, even the loss of a single alpha node could strand a superdreadnought, leaving it a sitting duck for follow-up capital ships to finish off. However, even against an "old-style" SD, the cruiser would have its work cut out for it. Although a Saganami-C could launch the number of birds you're talking about in a single launch, without Keyhole and/or Apollo, it couldn't effectively control them. They could send them all rumbling off down-range, and the missiles' internal seekers and targeting software are significantly better than was available in 1905, but once the attack birds drop into autonomous control, they become far less effective. Worse, managing the Ghost Rider functions in order to get the most out of them uses up a lot of control linkages and bandwidth all by itself.
In any case, the range advantage of the Mark 16, coupled with the acceleration advantage of the smaller ship, ought to allow the cruiser's captain to engage the superdreadnought without risking return fire. That would help in several ways, including the fact that it would allow the Saganami-C to stack salvos as large as it could effectively control and would eliminate the pressure managing missile defense would place on the cruiser's fire control.