You neglect to mention which kernel you're using but I'll hazard a guess that it might be M-Kernel because that's the only one that I know of (currently) that by default is set to use 2 cores - Metallice has a post in the M-Kernel thread where he states why he's chosen the 2 core default over 4.
Basically it comes down to the understanding that Android was designed for 2 cores and most - which means the overwhelming majority, mind you - every app that's out there will use no more than 2 cores by default, with a very few (like less than 10 or so) apps will seriously push more than 2 cores to any significant degrees.
2 cores = less power usage = longer battery life overall = doesn't make that much difference in regular day to day use of any given quad core Android-powered device.
All 4 cores kick in for a variety of reasons but when they do it's usually just temporary, a momentary spike in CPU power to handle something faster and then it's right back to idle/offline status. In general, the only thing you might notice is a tiny bit of lag with using 2 cores in starting up apps or other such momentary situations that can make use of more CPU processing power but then they end up shutting off again.
In the long run, having 4 cores is more of a luxury than an absolute necessity. There's a video on YouTube of a guy using a Samsung Galaxy Note II and running 4 videos at the same time on the device; that's about the only time he could get it to require all 4 cores being utilized and even then they were far from being maxed out unless he had some other stuff going on at the same time.
Your battery will thank you by utilizing that ROM's default of 2 cores - if you really really need all 4 cores you'll know it and you can easily enable the other cores with something like Trickster Mod which is what Metallice recommends for M-Kernel tweaking anyway (the only app he recommends, actually).
You really should read or at the bare minimum skim the thread about the kernel you're using, even if the thread is very long - it's more useful to read and learn stuff than creating new threads for such info which is generally frowned upon around here.
Self-research is the best course of action, aka finding out for yourself from the volumes of info this forum has.