There are still many things in SOC which Lua cannot modify directly:
* level headers (as already mentioned)
* cutscenes (not that anyone uses those kind anymore though)
* emblems
* unlockables and condition sets
* character select entries
* general game settings, such as the gamedata file or what SP stage you start with on a new save file
* fades (a feature new to 2.1)
So yes, SOCs are still a thing. And no, Lua does not exactly "replace" all of SOC's features, even the parts that most people used it for back in the day (that is, custom objects and states) are still usable with SOC (even Lua can do them too now).