Citing article where listed author is pseudonym
Always use the name that is used on the article/book you are referring to. 

If someone searches for an article referred to as being written by Dwork, but the name on the article is Boyarsky it will only cause confusion about whether this is the article they are looking for.

Regarding the pseudonym: I would not mention it at all. It is up to the author when or where they reveal that they use a pseudonym. Even when it is commonly known I would still not do this, except when you have explicit permission from the user of the pseudonym. This way you avoid spreading awareness of the use of the pseudonym in a situation where the user may not desire this. One exception could be when there is suspicion of the pseudonym being used with ill intent. Generally though I think it is good to be cautious about such revelations.