The short answer is that the Area 51 software was derived from the main Stack Overflow Q&A engine. The core functionality was retained (wherever appropriate) to maintain as much of the user experience as possible. Some of the functionality (like the badges you cited) may not necessarily make sense in this system, but little work was expended to remove this functionality and we wanted to keep the functionality surprises to a minimum.
Given that posters are actively discouraged from "Voting Up" questions
that have already got the requisite 10 votes (a Nice Question) what is
the point of retaining these?
Such 'active discouraging' is nonconstructive, so the question should be, how to deal with such discouragers? The problem is, there's no vote do delete comment and flagging for moderator attention each time is for many users too hard reaction.
In my opinion, each proposal needs at least a few really good question, and not 40 average ones.