I regularly get this:
It took 148.17 seconds to enumerate untracked files. 'status -uno'
may speed it up, but you have to be careful not to forget to add
new files yourself (see 'git help status').
How can I run git-annex sync without enumerating untracked files? Can I add the -uno switch somehow?

Well,
git annex syncdoes not itself rungit status.Try running git-annex with the --debug option, it will say what git commands it runs, and that should help find out which git command is complaining.
My guess is it's
git commit, which is probably getting the status unncessarily for a commit message template, despite a commit message being specified. If so,git annex sync --no-commitwould avoid that.