I file my returns jointly with my wife. But she started a single member LLC. She didnt have any income. Should we still file joint with a schedule C for her LLC?

An LLC is a Limited Liability Company. If she is a sole-proprietor, you can still file jointly. 

For tax purposes, the entity must be a sole-proprietor, partnership, corporation, or S-Corp. 

According to the IRS:

"Depending on elections made by the LLC and the number of members, the IRS will treat an LLC as either a corporation, partnership, or as part of the LLC’s owner’s tax return (a “disregarded entity”). Specifically, a domestic LLC with at least two members is classified as a partnership for federal income tax purposes unless it files Form 8832 and affirmatively elects to be treated as a corporation. And an LLC with only one member is treated as an entity disregarded as separate from its owner for income tax purposes (but as a separate entity for purposes of employment tax and certain excise taxes), unless it files Form 8832 and affirmatively elects to be treated as a corporation."

https://www.irs.gov/businesses/small-businesses-self-employed/limited-liability-company-llc