Q: Is Nissan removing these emblems or offering the delete as an option?
A: 
No.
Q: Are people removing them for some odd, insecure reason?
A: Partially. As texasrogue pointed out, it saves Nissan money by not putting the
S emblem on the base model. In 2017 Nissan sold 403,465 Rogue's. Assuming one third are the base model (134,448), and only half didn't get the emblem (67,244), and the emblems cost say $4
each, that's a savings of $268,976.
And then there's the vanity angle. Some people change their badges because they're embarrassed to be seen driving a base model vehicle. Case in point, when I worked at a Nissan dealership in Maryland we had a woman trade in a base model Rogue that she had re-badged as an
SL.