Positive energy only really matters for Antimatter. Since you asked I’m assuming you are not far enough in Space/Challenge runs/Religion to have unlocked the ways to make energy management much easier.

For pollution, I like having it at 0, but realistically, I know that I’m heavily gimping my production by doing so.

Energy deficit is not a binary on/off, most of the energy penalties are proportional to production/consumption delta. If you have large production and slightly larger consumption with minor deficit, the penalty should be a few percentage points.

Unlike energy, pollution has much fewer ways to manage, but for 99% of the players its effects should be negligible.