My Common app looks pretty good so far (5’s on APs and 800s on Subject tests, etc), and I noticed the class rank section is optional. I suffered from a lot of health problems in freshman year and my GPA suffered (it’s 3.75 now). In addition, I don’t have a high number of honors/college classes to increased weighted GPA. My class rank is probably in the slightly-above average for my school, and I don’t want to include it. Is that bad?
If I remember correctly, there is a section on the counsellor’s recommendation that asks about class rank, so whatever you choose, I would suggest trying to keep it consistent with what he/she inputs.
That being said, if you explain in your application what you just explained to us (that you suffered from health problems) I’m sure that colleges will not hold it against you.
Good luck.