Yeah, rocks in space don't appear to need a shielded torpedo. If they were filled with Borg slurm (as some of the stuff states), you'd think they'd be shielded. However, we do see them split up into fragments when near their target, which seem to cause significant damage themselves (each fragment). Multiple warheads to preclude them from all being shot down when incoming? Multiple warheads to cause as much damage as possible due to various systems being hit (you just need one BB to hit the eye...). That's one interesting thing I find about them anyway, and something a self-propelled mining charge wouldn't really need. You'd just need a big boom to fragment a rock up to a planetoid in size
I can't recall that scene, but if Starfleet thinks they can during a similar period, then shields or not probably don't matter (you couldn't really put much of a shield on a torpedo anyway). Yeah, from all the powers we see, having the shields as powerful as you can make them so that they can take the hit is how they go. Narada's torps easily breaching the shields seem to be their biggest point. For example, the computer simulation with the Klingon warbirds blowing up with a single photon hit once shields are down needn't be unrealistic -- simulations usually are accurate within a certain level of parameters. This could jive with Sulu warning about a second hit being catastrophic -- as we see from Kelvin, the torpedoes of Narada don't seem to be as actually destructive as the photons in the simulator, but they can get through shields. Enterprise probably could have taken the second one barring an unlucky hit, but that'd be academic, as Narada could kill her at her leisure.
You generally have to compute a heap of lead and whatnot when firing at objects crossing your bow. Whereas if they're coming straight on, it's often just point and click for the computer -- unless you have something I forgot about with Narada's torps, the multiple warheads that are released. Though this still wouldn't preclude phasers shooting them down as soon as they're launched. There's lots of precedence in our world of point defense systems not being switched on, even though they were technically able to shoot down the incoming missile fairly easily (USS Cole and that Israeli corvette. INS Hanit I think she was called). Enterprise, the Vulcan fleet, and Kelvin all probably weren't at combat readiness (just putting people on "Red Alert" isn't the same as being ready for wartime) -- this often happens when there's a single event that isn't deemed a wartime threat. I bet if Narada was still active, focusing phasers on the shield piercing torpedoes would be a priority (with stuff like photons used for anti-shipping work).
I recall Orci (?) stated Kelvin went to warp right at the last moment, though like with the Borg stuff, I guess that's not entirely canon. Still, Kelvin was one big damn photon. :P I guess throwing several starships at Narada with no crew and phasers set on maximum point defense, could at least knock the hell out of it so as standard weapons may eventually blow her apart.
I would have made something the size of Vengeance, but with dozens of fast firing photon tubes along the bow (big torps so as to have very big antimatter warheads and possibly a warp function, just way bigger than what Marcus had -- like mini-Dreadnought from Voyager without the weapons and a larger warhead; 1,000 kilograms of antimatter doesn't take up much space); standoff at range and sling them until empty. Warp back to a tender or base to reload, and warp back into the fray. Large magazines for the same torpedoes so to have decent endurance (take a look at Vengeance's hangar; you could fit hundreds of large torpedoes in there). Lots of point defense phasers on the dorsal and ventral surface, and with the saucer section more angled to a point, so most of the PD weapons can have LOS.