I agree that a second core would be useful on long-duration flights, but I dont' know about maintaining two in a ready-to-use configuration. Most starships perpetually have their engineering peons doing SOMETHING with the warp core in every shot we see it in; it stands to reason that keeping ONE going is a fairly encompassing job. Would a starship meant for efficient, long-duration space cruising detail that many MORE engineers to keep the second engine ready to go? Personally, I prefer the Voyager idea of having PARTS for one ready to plug'n'play, but still having the primary core the more efficient, more advanced piece of equipment. The secondary core would be smaller and less powerful, but at least it would let them get to Bespin.
Also, IN GENERAL the TNG tech manual suggests that a GCS warp core is used pretty much ONLY for the warp drive; everything else is run on fusion power. The idea is that the warp core is the only thing that can provide enough power, for the only thing that NEEDS that much power - the warp drive. Everything else, phasers, life support, whatever, is run off of fusion power. The only limits for things like phaser power is therefore not the enrgy available to use them, but the physical limitation of the hardware that can use it. You can shunt all the warp power you want through the phaser arrays, but why bother if you blow them out before they can even fire?
Of course, this would not necessarily apply to other starship designs, such as the E-refit's phasers which shunt power from the warp drive. THAT would be a case of using warp power to supplement fusion power to fire a weapon system that can handle more power than the fusion generators alone can provide, in that era. Give and take, really.
Mark