The commit graph of GitKraken sometimes contains identicons while some others contains the author's profile avatars for commits (I'm testing with GitHub, but I don't think it's specific to this instance).
I just can't figure out what makes GitKraken to decide (if any choice?) which one to show in each cases?
GitKraken uses Gravatar to decide which icons to show. You can read this up in the GitKraken help page on profiles and their FAQ (How do I change the avatar associated with my commits?).
From the Gravater documentation:
Thus, the committer email adress set up in your git config will decide which icon will be shown.