If you made contributions or withdrawals to an HSA in 2016, those must be reported on form 8889, and that form isn't ready yet.  If you leave the form out, you WILL get a letter and a bill for taxes and penalties, because if you don't use the form to say that you used the withdrawal for qualified medical expenses, the IRS will assume the withdrawal were not qualified and will charge you tax on them.  

You are correct that the IRS knows from the 1099-SA form that you had withdrawals, but they don't know that you used the money for qualified medical expenses unless you use form 8889 on your tax return to certify that the money was used for qualified expenses.