When you say "double panel", I assume you mean two panels side by side. IMO, it is best to do what makes the workmanship look the neatest.
If you lack neutral lugs in the first panel, it may be best to run the neutrals with the "hots" originating from the second panel.
As far as being concerned with inducing currents in the nipple, simple accounting rules out that possibility either way you go.
I see no point in automatically running the neutral with the "hot" in the second panel unless you identify both wires with the same identification. The exception to that rule would be if you you had a conduit entering either panel with circuits terminating in each panel. In that case, I would definitely keep keep them separate by banding each bundle near conduit opening with electrical tape or tie-straps.