The Daikiba/Shinkiba mission was changed from kills to points when all of the mission rewards were "rebalanced" a while back. That and the Cornundacauda one are the only ones that have been changed, up to now.
I have mixed feelings about changing more of them. On one hand, as someone who's already completed most of the kills missions I'd feel somewhat aggrieved that I had to do it the hard way while people doing them later get the same rewards for less work. The Cornundacauda mission, if I was doing it now, would take me half the time it took when I did it (or even less), and the Daikiba one is trivial now for anyone who's comfortable on the Stalkers. On the other hand, for the few kills mission I haven't yet done, I'd be more than happy to do them more quickly with a points based system. Scipulor, for example, I'd much prefer to do on high maturities but that makes it a very long mission with the old system. I might even finally finish the bloody Hiryuu
If they're going to change them they should just do it all at once, not one by one. Now that they've changed the Cornundacauda one I'm reluctant to work on any of my unfinished kill point missions, knowing that they might be changed to points in the future.