hardwood door thresholds
I have it running both ways in my house. One hallway runs parallel to the joists for ~13'. It's also running parallel thru my living room and dining room which is a ~27' stretch at max. This is white oak strip flooring, 60 years old in the living room/dining room, no obvious indication of where the joists are (due to sagging I assume). I've also seen it running two different directions in other houses, so it might be common enough to run it parallel?
I'd say as long as you have a solid & strong subfloor it won't be enough of an issue to matter. My subfloor is ~60 year old 1x12's nailed down perpendicular to the joists. If you are worried about yours, now is the best time to strengthen it.
But then again, I'm not a pro.