It certainly will depending on where the applicant is from. If lets say she's Canadian and the spouse is American then likely not an issue lots of people get married that way. If lets say one is Indian for example then that will raise red flags. Think about it, if you were to do marriage for just the purposes of immigration you wouldn't want to go all out and draw attention to all your family, friends and the community, you would just do a civil ceremony. So it just makes it a little harder because it opens you up to questioning "why was your family not there?" "why were friends not there", "its normal in your culture to do ceremony xyz….why didn't you do it?" So that is inviting more scrutiny.
Remember that you don't just have to prove your marriage is legal for spousal sponsorship...that's easy.....you also have to prove your relationship is genuine.