In Dexter Season 5 Harrison's nanny looks like an important part of the story. She is the only one who passed the nanny interview held by Debra. She really even cares for Harrison. So why did she disappear in the start of season 6 ? I am unaware if it's mentioned later.
The Wikia page for Sonya also adds
Sonya unfortunately fell into the category of characters that disappear between seasons. This is likely due to their contract only requiring their appearance for one season and/or Showtime deciding to drop them afterwards. It's assumed that Showtime felt a younger, more visually attractive woman was needed to replace her for on screen appearances.
According to IMDB, she took up another role Corp & Anam after season 5, so perhaps she was only contracted for 1 season and couldn't be obligated into another season.
I wondered this as well. I would assume it was because Dexter's late night activities caused a problem. Remember she had already quit once and warned him. He probably left her holding the bag again, like he often did to Jamie as well. The plot line likes to emphasize his role as a parent, but he often was an absent father, getting home with barely enough time to tell his child goodnight and often still letting the nanny tuck him in, then leaving again to go kill someone.
From Entertainment Weekly, showrunner Scott Buck answered it himself:
Dexter’s son, Harrison, has a new nanny named Jamie (Aimee Garcia), who is the younger sister of Angel (David Zayas). First of all, what happened to Sonya (Maria Doyle Kennedy), the old nanny?
She was such a fantastic actress but we had kind of wasted her in a way that she wasn’t given enough to play, and it felt that by this time it was already a lost opportunity, unfortunately. We thought it was best to move on in a new direction.
So it seems they didn't see any potential for her future arc.