NFPs or Non-Functional-Pads are often removed for SI reasons (reduces via capacitance). Other reasons are also in play. Typically you would handle NFPs either in a pad-stack-editor at the layout level or simply suppress them when generating gerbers.
I am all for the simple solution of suppressing NFPs when generating gerbers. I know of no good reasons to keep the NFPs. Especially once you start removing some of them.
Right click on pad → Properties → General [Tab] → Copper layers: [Drop down list] → choose “connected layers only”
Is that what you are thinking of?
I don’t know if it is possible to set this as a general setting for pads. At least it can be done for individual through holes.