If you connect a fully charges cap across a fully discharged cap the total energy that remains in both caps after everything is settled is half as much as you started. If the wires are ideal and there are no resistances, the energy dissipates into the atmosphere in the form of EM energy, light, heat and sound when a spark happens.
That cannot be right. Assuming the system is ideal there by definition will not be any losses. So no heat, no light no nothing related to any imperfection in the connection itself.
If we are extremely strict, then yes all accelerated electrons do radiate EM quanta and you can't move the electrons from one cap to another without accelerating and decelerating them.
Hmm, let's think about that for a moment... OK, heat and light are EM radiation so while there are no losses in an ideal system, the acceleration radiation technically qualifies because it is a property of quantum mechanics and EM in nature. Also now that i am thinking about it, there are 2 further possibilities; either we assume the connection to be totally lossless or then there are wires that have a distributed inductance and capacitance. The wire capacitance can be assumed to be not significant but the inductance will create a lossless resonant circuit with the original caps.
So in the case of no inductance and no resistance we will have one hell of a current pulse when the charge carriers balance (no losses remember). I am too lazy to think how to calculate the current magnitude, but probably you need to do it the hard way from first principles. Electric field force accelerating the mass of an electron or whatever you want to use as the charge carrier. Nope, too lazy to start that. The peak current will anyway be _high_.
And if we do have inductance, there will be a lossless resonant circuit. Only not totally lossless, because accelerating the charges back and forth will again cause EM radiation only on a vastly lower scale than in the previous case. So eventually this damped oscillation will stabilize (provided the universe lasts long enough) and the charges in the caps will be equal. Of course i just say so; a lossless oscillation never stops but at least you can calculate the limit value where the stable point would be.
Without actually calculating it i am prepared to accept that the remaining charge in the caps is only half the original. The main thing was that the energy does not "disappear" into nevernever land.
It is a bit surprising but on the other hand it shouldn't. I vaguely recall some theory related to power transmission, where you can only get maximum of half to the other end. Been too long, can't really recall any more but must be the same thing...