There are many reasons why someone writing plays in Elizabethan England might use a pseudonym and the use of a pseudonym does not exclusively mean the author of Shakespeare's plays was a woman.
If we accept that Shakespeare was not the author of the work penned under his name, it is just as plausible to suggest that the author was, in fact, a man of high social standing. The theatre was seen as an immoral and lowly pursuit at the time. An aristocrat writing plays might also adopt a pseudonym to protect his reputation.
However, the far simpler conclusion is that Shakespeare, the glover's son from Stratford wrote the plays. If 80% of plays were left anonymous, why would an author that wished to hide his/her identity bother to find someone to put their name to it at all? Why not just publish the plays anonymously? This would likely be far easier (and cheaper) than paying a Stratfordian bard to put his name to the works.