Marvel, in their comic books use the word "nannite", whereas in most other science fiction use "nanite" for their nano-scale distributed tech.
I too, think it's dumb, but I would prefer to stay with the source material's spelling.
Are you sure it's safe to assume "nannites" is the general spelling used in all of Marvel and wasn't exclusive to Uncanny X-Men #446? Because most comics I've read that talked about nanites, they used the word "nanites" (issues from She-Hulk, World War Hulk, Hulk, Dark Avengers, All-New Wolverine and X-Men: Gold are some examples I can provide). If that's the case, I don't think it's bad to assume "nannites" is a misspelling or an alternative spelling which could be ignored.
Fair. It's in multiple issues, but it's probably only Chris Claremont's comics.
The article in question (Sage (Earth-616)) is 90% Chris Claremont's comics so you might not be surprised that all my research for it saw just the one spelling.