You can always try ETTR to lower noise levels even more if it's bothering you, and for longer exposures it's better to stay at lowest ISO possible, especially with older cameras that might suffer more from heat and read noise issues.
Noise will always be present if A) you shoot at high ISO, and/or B) you underexpose your image (even slightly). You can still shoot at ISO 1600 and get little noise if you get the settings right and the scene helps you as well, but as soon as you get some dark areas and push shadows in post you will see it clearly as day.
There is no universal right or wrong nor is there a setting combination that will always give you little noise. You need to deal with tradeoffs as settings all depend on the scene you are shooting and the result you want to achieve.