So this issue has been reported on Sophisticated Storage github a couple days ago, but for completeness sake I wanted to report it here just to make sure you're aware of it here too.

As of a fairly recent (sorry for vagueness) update to Sophisticated Storage, EMI's recipe tree highlight stopped working properly with storages opened from the SS mod. Salandora in that other thread found and explained the issue, that it's because SS storages have potential to have a crafting station (via the appropriate upgrade when added to their chests), their entire storage of items counts as if they're already in your possession to craft with, regardless of whether the interface is actually able to craft at the moment or not (i.e. has the crafting bench menu open or not).

See Salandora's comment for further info here:
P3pp3rF1y/SophisticatedStorage#674 (comment)

I could find the issue explained in code in EmiScreenManager's renderSlotOverlays, however, I couldn't find a EmiGridMenuInfos function or file anywhere that they proposed a fix for, so I'm not fully sure if this issue is to be fixed on EMI's side only, so apologies if it doesn't quite fit here.

Edit: I searched for EmiGridMenuInfos and EmiGridMenuInfo (thinking the infos might've been a typo in Salandora's comment) in EMI and sophisticated storage codebase, but unfortunately when I thought to search for it in sophisticated core, I only searched for EmiGridMenuInfos. EmiGridMenuInfo is indeed present in sophisticated core and I can find the place they suggested replacing the getInputSources function to fix this issue.
So if that's the case this might be a fix entirely on sophisticated storage/core's side, but I'll leave this open just in case there's anything about it to be done on EMI's side.