I've been using APE since it came out and never, not once, has it ever caused me a single problem. I use a host of Unsanity products as well as other programs that use APE. Again, no problems. Neither have I had any problems with this most recent version of ShapeShifter.
As for performance issues, I've found that it depends on the theme. Some themes I've used actually (at least subjectively) make my Mac seem faster than it does without SS. Seti, in particular, is exceptionally fast. So are Muku, Aluminite, iMetal, Cold, X-Metal, and Quad. I don't know why some themes bog my system down and others do not. But I do think that the speed issue needs to be examined in this light. Kaleidoscope themes had a similar range of performances.