I haven't ever been able to tell the difference between a pasteurized or non as a juice base in the final product.
I've also made quite a few batches using store-bought, filtered, pasteurized juice (i.e. the big jugs of "no preservatives" stuff on the bottom of the shelf in the grocery store). THAT stuff still can make a good final beverage, but it turns out quite a bit different than the fresh-pressed stuff.
In particular, the store juice tends to be much more tart. That can either be exactly what you are looking for or something to compensate for.