Applied optimizations:

1) Used cached get() method instead of indexing. This optimization already was used in update() and subtract().
2) _keep_positive() is optimized for the case when most counts are not positive (common case for substraction and intersection).
3) __add__ and __or__ are defined via inplace operations which are faster (due to fast copying and _keep_positive()).
4) Inlined and simplified the code for __pos__ and __neg__.

May be following optimization can be made by implementing _keep_positive() in C.