You can print or record Disbursements (non-Payables) Checks to 1099 vendors if you wish. A Disbursements Check is recorded as a 1099 payment if you mark the "Record on 1099" box in the Disbursements Checks window when you enter the check.
Disbursements Checks to vendors are not posted to Payables because they are not Payables activity. To show vendor activity on Payables reports, enter the activity through Payables.