It doesn't matter.
Odds are if the relationship becomes serious or they get married they may visit each others church or one may decide to join the other's. However it shouldn't matter anymore than if two people worked for different companies. In the event they one day have children together they may want to attend church as a family.
Nevertheless if you're only "dating" one shouldn't feel obligated to switch churches every time they enter into a (new) relationship. Most dating relationships don't lead to marriage.