git-annex has never used SHA1 by default. But, there are concerns about SHA1 collisions being used to exploit git repositories in various ways. Since git-annex builds on top of git, it inherits its foundational SHA1 weaknesses. Or does it?
Interestingly, when I dug into the details, I found a way to make git-annex repositories secure from SHA1 collision attacks, as long as signed commits are used (and verified).
When git commits are signed (and verified), SHA1 collisions in commits are not a problem. And there seems to be no way to generate usefully colliding git tree objects (unless they contain really ugly binary filenames). That leaves blob objects, and when using git-annex, those are git-annex key names, which can be secured from being a vector for SHA1 collision attacks.
This needed some work on git-annex, which is now done, so look for a release in the next day or two that hardens it against SHA1 collision attacks. For details about how to use it, and more about why it avoids git's SHA1 weaknesses, see https://git-annex.branchable.com/tips/using_signed_git_commits/.
My advice is, if you are using a git repository to publish or collaborate on binary files, in which it's easy to hide SHA1 collisions, you should switch to using git-annex and signed commits.
PS: Of course, verifying gpg signatures on signed commits adds some complexity and won't always be done. It turns out that the current SHA1 known-prefix collision attack cannot be usefully used to generate colliding commit objects, although a future common-prefix collision attack might. So, even if users don't verify signed commits, I believe that repositories using git-annex for binary files will be as secure as git repositories containing binary files used to be. How-ever secure that might be..