I'd understand not using Totsuka since it'd seal Kabuto before he got the chance to break ET.
But...you're right about Yata...it would've helped against Kabuto and wouldn't do anything to kill him either...
The explanation people have is Itachi trying to prep Izanami by creating a loop using the senses but that could've been done with Yata if used in a tough spot as well. Such as Muki Tensei and Tayuya's genjutsu right? No need for him to have let himself get hit that way if that wasn't part of the loop he was trying to create.
Not like I believe that Yata can take attacks that are too strong though but Kabuto doesn't have what I'd consider to be strong enough attacks...IMO anyways