Is use of unconventional design elements or layout something frowned upon in academic context?
Good design is invisible.  The goal of design is to increase understanding/clarity. If your design is truly good then it will go unnoticed but your content will be better understood.  If your design is noticed and distracts, then it is bad.  I feel these principles are universal.  

So to answer your question, yes, good design is worth it (it increases the amount that your content is understood), but just adding "design" elements without a good understanding of the audience and their expectations will not likely result in good design.