After some testing, it turns out that it's not quite the mod apocalypse I was fearing. The sim below is basically "Lady CC": her eye colour and hair and many of her clothes are cc, I used a height mod to make her slightly taller than most sims, and none of it is causing any problems.
https://abload.de/img/matriarchinbeneziai6ef3.jpg
I should mention, though, that her eyes are just a darker shade of blue that I made, not a default eye colour replacement. I don't use replacement mods, so I can't say anything about those.
https://abload.de/img/liaraalskleinkindkqdt5.jpg
I also played around with toddlers and infants in CAS, my cc for toddlers is still there and working fine. For infants I don't have anything yet, obviously, but no issues either. So I think regular cc that doesn't alter already existing things shouldn't be affected by the update.