Can someone explain how NS upgrades work? I know it says during the upgrade we won't have access to our account but are our integrations with Shopify/celigo all still running? Do those orders still come in or do they get stuck somewhere?

Typically, they'll queue in Celigo then start importing again once NetSuite is available. You should, of course, check that it occurs.

Yes this is what happens. Celigo will keep the records in queue until NetSuite comes back online.