Hi Kate,
The Cryptomatte plugin won't do anything useful in Arnold with deep EXRs, but even if it did the Nuke plugins would be unable to do anything with that. Deep Cryptomattes just aren't a thing (yet).
Thanks @Jonah Friedman, I was afraid someone might say something like that.
I saw a screenshot in a tutorial somewhere (maybe it was anderslanglands site) that shows V-Ray having a "use deepexr" checkbox in cryptomattes AOV properties, so I figure it's just Arnold - Nuke relationship. Maybe.
The funny thing is I can see deep cryptomattes in nuke's viewer in the upper left corner's dropdown. Just not in the plugin itself. Shame though, it would be awesome... rendering out the same thing twice is just a waste of time and energy.
thanks again
best
Kate
Not sure what you're remembering there, but I can say somewhat definitively that there has never been a deep Cryptomatte in any renderer, nor any compositor plugins that could read them, nor a Cryptomatte standard that applies to deep images.
Just because you can see something in the AOVs doesn't mean the data is there, those are probabily the "preview" channels you're looking at. To render shallow Cryptomattes with your deep renders, you only need to write out your Cryptomattes using a different driver, and don't need multiple render processes.