Since you didn't specify which kind of poles you're talking about: there is a specific reason that North and South magnetic poles are named as such, unrelated to why we consider North to be "up" by convention geographically.
"North" is the direction a North-seeking compass points to, and "South" the direction a south-seeking compass points to.
A bar magnet has two poles: a magnetic north (where magnetic field lines point outwards) and a magnetic south pole (where magnetic field lines point inward). A magnetic north pole is attracted to a magnetic south pole, and vice versa. So a compass needle, which is a magnetised metal needle, will point towards a magnetic pole of the opposite sense to that of the magnetised tip of the needle.
The Earth's magnetic field has a magnetic south pole located in the Northern hemisphere, and a magnetic north pole located in the Southern hemisphere. So a compass magnetised with a north magnetic pole at the needle tip will "seek" the Earth's magnetic pole in northern hemisphere, and vice versa.
The physics of magnetism was not understood historically in order to decide the naming convention for the geographical directions, rather the sense of magnetic poles were named to match the geographic sense later on when the physics was understood.