For SEO : No.
For user experience : Yes. which can lead to lower SEO results due to bounce rates going up and time on site going down.
The question you should ask yourself is this : Is the increase in profit from the popunder worth the possible decrease in SE traffic?
If it was my site, Id be saying a big NO to popunders. All they tend to do is just bother the potential customer.
True, but if as a money making site, popunders are a big earner.