Just wondering if the bore can be honed? She has a few lines in it so im wondering if it can be honed lightly or does that ruin displacement/quantity of air flow from the charger?

Unless there are heavy score marks inside the rotor housing of the blower then I wouldn't worry about it. To do the job properly the surface would need to be built up and precisely honed. Hone it alone, and you'll end up with an under performing supercharger to what you have now.