You issue a 1099-MISC for payments of more than $600 to LLCs, unless the LLC has made the election to be treated as an S- or C-corp. However, you should ask them to fill out a form W-9 for you. They can check the box for LLC taxed as an S- or C-corp and then not provide their EIN, but that way you have their signature on file that they told you they are exempt from getting a 1099-MISC. (If you take their word for it, and don't issue a 1099-MISC, and they are lying or mistaken, you can be fined for not issuing the 1099. If you get the W-9 where they sign that they are an LLC taxed as an S or C, then you made a good faith effort to do the right thing.)
If they are exempt from receiving a 1099-MISC, then you simply don't report their income to the IRS. They are required to accurately report their income and pay tax, and whether they do or not is between them and the IRS.
