One of Shakespeare's central points in Twelfth Night is to show that things really are not always what they seem to be, plus to show the consequences of deception. Hence, nearly every character at some points conceals reality behind some type of disguise, leading to various consequences.
One of the most obvious examples is of course Viola disguising herself as a boy servant. Viola made the decision to disguise herself out of self-preservation. She arrived in Illyria as an orphan after surviving a shipwreck. Her father died when she was thirteen, and now she believes her brother, her one remaining guardian, did not survive the shipwreck, leaving her all alone. More importantly, she is also a wealthy noble woman. Hence, she knows that her wealthy, orphaned status puts her in a very vulnerable position. She first expresses her desire to hide her true identity in order to protect herself in her lines:
O that I served that lady [Olivia]
And might not be delivered to the world,
Till I had made mine own occasion mellow,
What my estate is! (I.ii.43-46)
But when the sea captain advises that Olivia would not admit her into her household due to her state of mourning, Viola instead devices her plan to disguise herself as a eunuch and go to work for Duke Orsino.
Naturally Viola's choice leads to a couple of unanticipated consequences. For one thing, she falls in love with Orsino and cannot proclaim her love for him because, for one thing, she is pretending to be a boy, and for another thing, she is pretending to be his servant, and servants of course cannot marry nobility. The second unanticipated consequence is that Olivia falls in love with her as a boy, which means that just as Olivia is breaking Orsino's heart, Viola is now put in the position of breaking Olivia's heart, a position that she certainly does not really want. Hence we see, just as Viola herself later exclaims, "Deception, I see, thou art a wickedness," just how much damage disguise and deception can cause (II.iii.26).