Yes you have 3 years to amend if you are getting a refund. No time limit if you have a tax due but the tax due is still due by this April 15, 2025. So if you think you will owe you should pay some to the IRS online. Did you actually file your Joint return? Then the extension doesn't matter anymore.
If he has a Net Profit on Schedule C he will owe about 15.3% Self Employment tax on it in addition to any regular income tax. So I expect you will owe on the Amended return.
