You should file the 1099s IMHO... And the reason isn't the penalty.
First, your tax return asks a couple of very specific questions about whether you owe people 1099s and will file them... so you have to lie once or twice on your return. That's a bad idea... Probably the IRS computers will be able to guess that's happening and will bump your DIF score for that. (The DIF score tells IRS which returns are most likely good returns to audit.) And if you do get audited, you don't want to have little lies like this shadowing the rest of the audit.
Second, your filing of 1099s probably supports your treatment of the vendors as independent contractors and not as employees. By filing 1099s, everybody (IRS, employee, you) have official paperwork that says, "Yup, these guys were not employees. They were independent contractors."