I\'m trying out SpriteKit with the following setup:
It seems to be a bug with the SKEffectNode trying to apply a filter on children SKShapeNodes as far as I can tell. I played around with this and achieved your results, but when I switched out the SKShapeNodes for SKSpriteNodes (using a simple png of a circle) the cropping no longer appears. It's a bug in that SKEffectNode doesn't handle the stroke of the SKShapeNode very well. If you take off the stroke (lineWidth = 0) and give it a fill color, you'll see that there is no cropping.
As for the frame rate, SKShapeNodes perform poorly. Doing the switch to SKSpriteNodes I mentioned earlier boosted my fps from 40 to 50 when I had 35 nodes on the screen (iPhone 5) with the filter applied.