Have you been cheating?
Let's back up a bit. IRS rules require that you begin witholding taxes from any employee after you pay them $600 in one year. Your one 'escape' from this is if the payments were made to 'contractors,' rather than 'employees.'
The W-9 form is used by your customers to document that you were a contractor, and not an employee. If their books are checked, the W-9 is another link in the chain.
1099's are another matter. Keep in mind that the customer is under no obligation to send YOU a 1099. It is very possible that an audid of your books might have, as its' original reason, a desire to confirm data provided by a customer; the customer might be the real target. If the ABC Co. claims to have paid you $50K last year, and your records indicate you only billed them for $1K, there's a problem somewhere.
A similar type of investigation has resulted in some simply massive enforcement actions against illegal workers and their employers. Joe Smith is asked why he failed to report wages that he never received - the employer was using Joe's identity to 'document' an illegal. The employer usually gets this information from job applications.
I would not woory about 1099's. I would worry about providing your accountant with accurate information.