Will I be penalised if my economics job market paper is coauthored with my supervisor? I read once before that the job market paper should not be coauthored with my supervisor because other universities will assume that my supervisor did all the work. 

I will apply for an academic role after my PhD, is it true I will be penalised for this?

If my other two papers are relatively strong will that eliminate the risk? 

But what if my supervisor coauthors on more than one paper?
Economics is not my field, so my answer is based on what I've heard from other people. Generally, it is preferable if the job market paper has a sole authorship or at least if it is co-authored by other graduate students. However, I have heard of people getting jobs even with a job market paper coauthored with their advisor. Since you have two other papers, and one with sole authorship, that will to some extent work towards eliminating any negative impression that the job market paper may create. However, ultimately it will depend on your potential employers and the practices that they follow. Keep your fingers crossed and hope for the best.