*dons magical scholar hat*

Well, it's been shown on the show that magic itself is a type of energy, right? Unicorns have it, they seem to run out of it when casting too many (or too difficult) spells, and they eventually regain it through biological means. So there is some form of energy to power whatever effect happens.

On top of that - while we're mentioning the D&D system - what about the multitude of different planes? What if the "destruction" is simply the thing getting broken down, then shunted to some plane where its components will be turned into whatever makes up that plane? Or in the case of Neighcromancy, I seem to remember those spells were powered by snagging Negative Energy from the Negative Energy plane.

So while from our perspective in Equestria, it may well look like - and function for all intents and purposes - as creation/destruction, I'd wager there's sufficient things going on in the background that can offer an explanation.

Just a thought that might help settle things.