Yes you could use the Employee expenses deduction as well as the Home Office Deduction, as long as no expenses are double counted.
However, there is a catch: For the Home Office deduction for Self-Employed, you must regularly use part of your home exclusively for conducting business. For example, if you use an extra room to run your business, you can take a home office deduction for that extra room.
If you used the same area for both W2 and 1099-NEC income, you would disqualify yourself for the IRS Home Office deduction. (See The Home Office Deduction - TurboTax Tax Tips & Videos)
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