1) me and my wife are the only owners of an scorp that did not make a profit this year (it made a small loss).

2) I have another paying job that issues me a w2 but my wife does not.

3) I want to pay my wife via a 1099-misc so we can claim the child care deduction (I don't think you can claim this deduction if your wife does not have a paying job).

Question: Can I pay her via a 1099-misc from the scorp that she owns, and does it matter that the business posted a loss this year and this 1099-misc that I pay her will increase that loss.

“3) I want to pay my wife via a 1099-misc so we can claim the child care deduction (I don't think you can claim this deduction if your wife does not have a paying job).”---->No; an S-Corp shareholder/owner does not get a 1099. You get a Schedule K-1, showing your portion of the income and expenses from the corporation. Owners of the S corp who work for the corporation should be hired and paid on a W-2 like any other employee would be. If you ,the S-Corp, don't do this, the IRS will come along and tell you how much you should have drawn, then hit you with penalties and fees for failure to withhold taxes.Correct; You (and your spouse if filing jointly) must have earned income to claim child dependent care credit during the year.
“Question: Can I pay her via a 1099-misc from the scorp that she owns, and does it matter that the business posted a loss this year and this 1099-misc that I pay her will increase that loss.”---> Your S-corp has to file its own tax return, and will give you/your wife a K-1 form which will be used to transfer the S corp income to your personal return. You don't use a 1099. By definition if you/your wife provide services to the S-corp, you MUST issue yourseves a W-2.The IRS would have field day with you 1099-Miscing yourselves.