Are you sure about that? Can you post a screenshot of one of their product details pages?

Export your inventory from Lightspeed and don't change anything in the csv file. Open excel and click file-import then import it as a CSV, comma delimited, and select text formatting and it'll show all of the leading 0s 

Have you tried opening the exported lightspeed csv file with LibraOffice?

Does your checkout work with Shop Pay?