PAL NES hides the left and right 2 pixels by design, no matter the screen. This is includes a modern flat screen TV. So you'd probably want to avoid any important information there.
For the rest, just use common sense. If part of the window border is missing, it's no issue. Text shouldn't be placed on the left or right corners, though, even though Castlevania III does this, and it DOES look ugly on my real PAL NES. Many Squaresoft SNES games such as Chrono Trigger also place window border at the very left and right edges of the screen.
What I'd say is try to keep the left and right borders clear, if you can. If and only if somehow you have to lower the quality of your translation significantly because of this limitation, then do enlarge the window and don't ever come back to this decision.