The long hours issue is not unique to startups. I've seen happy couples where one partner works long hours and the other does not, and when both work long hours. But obviously it depends on the couple and what they both want out of life and the relationship.

The issue that is more specific to startups that can arise is money. Bootstrapping a startup can involve lower or no pay for an extended period. Both partners need to be on board with that, since money is apparently one of the main things most couples argue about!