The assertion was that it deters the AI. So, player behavior is beside the point; obviously, a player is going to do it if he/she want to. But, actually, the fact that it annoys you (and me and probably others) DOES probably deter us a bit, too.
As to how effective it is at deterring the AI, it was incredibly effective in previous patches. I can't swear how effective it is in the current version, since they reportedly tweaked it (1.7, IIRC). I would doubt that they removed the deterrent logic, completely. I suspect they just toned it down.
National ideas may not be the best tool, but it seems to serve. Since it's not a mechanic that is particularly egregious or broken, IMHO, I'd hope they focus on other improvements first.
To wrap this up I would prefer attrition, nationalism, maybe even a local autonomy modifier instead of the coring cost.
But you're right there's bigger fish to fry right now.