If these are structural parts and take either a tension force either parallel to the long axis, or a shear along the short axis, printing them vertically makes no sense. Yes you can reinforce them later but then the 'reinforcing' will be taking all of the load and the 3d print will be purely cosmetic. I don't care what anyone says about the layer bonding of nylon it's still FDM and the layer lines are considerably weaker. Besides, that's a really long part and nylon is a floppy noodle compared to most other 3d printing plastics, what exactly is this part going to do?

Printing them horizontally is going to have more risk of warping, but makes more sense structurally. Could you draw a quick diagram of the part (a rectangle will do) and the forces you're expecting it to take? That'll help decide which orientation to print in. For some cases it might even be beneficial to print them vertically.