Writing back may not change their list, but writing back to reconfirm your interest does remind them about you, and if you made a good impression, keeps you fresh in their mind when the time comes to making a rank list. Just consider it another opportunity to communicate with them.
If the email came from the program director, call them back and tell them over the phone. It may be a formality they send to everyone, but it can serve as an invitation to talk with them again, which is almost like a mini, second interview.
I told my top three programs that I "were ranking them at the top of my list."
When I finalized my list, I emailed my #1 and actually told them that they were number 1.
Can it bite you if you tell everyone that they're number one?
Absolutely. If they don't fill, for whatever reason, and they ranked you, then they know you burned them. Not filling is an embarrassing situation for a program director to explain, especially at a top program.
Happened to me. The three programs I told were "at the top of my list". . . the one I ranked third took it to mean they were literally the top of my list. It was a new program director who was trying to really shape the personality of the incoming class, and didn't rank enough people in the end. It was a rookie mistake that came from not being in the system before to realize how many to ultimately rank.
They didn't fill. . . I had to explain it to him (he's a friend of a friend, so he felt kinda burned).
Not something to generally worry about though.