There's no reason not to fly NH from a mileage accrual perspective. If you buy the ticket from UA, the flight will credit just as it would on UA. If you buy it from NH, you won't get PQD and mileage (RDM) will be calculated based on miles flown rather than dollars spent.

Advance seat assignment is not an issue (though if you are in economy and not on a full fare Y or B, your choices will be restricted).