I always had to solo and bounce one at a time.Create a set of groups in Cubase (or 'auxes' in Pro Tools, not sure what it's called in Logic) and send the output of each desired set of instruments to a dedicated group. I haven't tried this on Cubase/Nuendo, but Logic couldn't pull this either. I think 'Stems' in this scenario relates to the music terminology, so all the 'Drums' will be one stem, 'Bass' would be another, 'Guitars' and so on. I always had to solo and bounce one at a time. So what the OP wants to do is, when bouncing say 'Synth Pads' which have a 'Kick Drum' side-chained to it, ducking the pads every time the kick drum plays, on exporting the 'Synth Pads' don't have the side-chain effect of being ducked. Done.I think 'Stems' in this scenario relates to the music terminology, so all the 'Drums' will be one stem, 'Bass' would be another, 'Guitars' and so on.

What we in post do is we route outputs to groups and render those as stems, so if that's what you do then just create an additional send and set its output to that group that you're rendering. If you're using a 'send' to get your signal to a side-chain input, then really the only question is how you capture your 'stems'. It seems to me that this should be very simple to achieve. 'Stems' is a term that was adopted from post audio and misused (in my opinion). It's not really clear what you mean by stems though, or 'stem busses'.

Cubase 9 pro sidechain not working