You should fill out the W-9. For the company you are working for, this is a legal requirement. You are correct that they will send you a 1099. However, if they were paying you through the merchant service, you are not required to enter the information twice as part of your self-employment income, as it is a duplication: the company states how much they paid you (no matter how they paid you), whereas the 1099-K describes how much you received through the merchant services. Where these items overlap (the company paid you through the merchant service), you report the amount the company paid you and later deduct the fees you paid the merchant service. You won't pay extra tax, but the correct tax. But the company needs your W-9 or they will take out backup withholding (28% of the amount they paid you) to the IRS, which you will be responsible for.
The specific situation in your question does not deal with a W-2. Form W-2 is for an employee, which at least for this particular company, you were not. You were a contractor which falls under the category of self employment. Here is an FAQ with more information on this: https://ttlc.intuit.com/replies/4771022
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