Yes, amend your 2018 return to include your missing $3,000 non-deductible IRA contribution. While it is true that your tax due amount, if any, or refund amount, if any, will likely not change, your amended return will be more accurate than the original because you have included Form 8606 with the amended return. And yes, include Form 8606 with your amended return and double check Form 8606 to ensure that your non-deductible traditional IRA basis is accurate. Note, that the traditional IRA basis carries over each year, thus, you may need to review Forms 8606 for more recent years to ensure that basis is correct.
Your amended 2018 return will need to be paper mailed to the IRS. Amended returns beginning with tax year 2019 can be e-filed but prior to that date, amended returns must be mailed to the IRS.