Do medical expenses paid with HSA funds count towards calculating deductions?

No, you can't deduct the expenses if you used HSA funds.  But, TurboTax will calculate this for you.  

You should include all of your medical expenses in the medical expense section (Federal > Deductions & Credits > Medical Expenses), and then the HSA withdrawals (from 1099-SA)  used for medical expenses will be removed from the total.