My friend and I have gotten 60+ stars so far on the split screen hack. We haven't had a huge amount of problems. The issues we did see, such as: clipping through walls getting stuck in limbo after you die and general difficulty controlling the death bubble, as well as camera issues with the camera getting locked in a floor or failing to go into first person for the cannon, were all solved by getting the star or pausing and exiting the level.
At one point, we tried and failed about a hundred times to jump from pole to pole in the volcano before realizing that there was a platform near enough to land on and bypass the problem. We haven't had to skip any stars yet, But the next star is the one in Bowser's sub cavern with the moving poles, so we'll see how that goes.
The split screen hack might add a bit of slowdown and weirdness here and there, but it is absolutely one of the most fun ways that I've ever played Mario 64. It works on flashcarts and emulators, so give it a try if you get a chance.