It strongly incentives people to not explain themselves, not open themselves up for debates, but just vote and then remove themselves from the discussion.

This is exactly the reaction I want to trolls, basic questions outside of dedicated posts, and stupid mistakes. Are downvotes of explanations in those cases also read as an incentive not to post explanations in general?

Do you think that's a good thing, or just a likely outcome?

Comments can serve as calls to action encouraging others to downvote or priming people with a negative or unintended interpretation of a comment - be it yours or that of someone else -that influence is something to be discouraged. This is not the case with all explanations of downvotes but it certainly describes the effect and often intent of the vast majority of "Downvoted because" declarations. Exceptions include explanations that are requested and occasionally reasons that are legitimately surprising or useful. Obviously also an exception is any time when you actually agree they have a point.