The two pickups have magnets and a coil.
The magents can have north on top or south on top. Rotating obviously doesn't affect this.
They could be wound clockwise or anti-clockwise, again rotation doesn't affect this.
Humbucking 101 in case anyone isn't up to speed:
The 'hum cancelling' effect of a humbucker is normally achieved by either reversing the magnets of one pickup and connecting its coil the other way around. This means the two (magnetically induced) signals from the strings will be in-phase and add up, while any electromagnetic fields causing hum in the coils will be out of phase cancel out.
As well as often having subtly different windings or pole piece spacings paired pickups (like on a Jazz bass) are normally set up like this to give a humbucking effect.
If the pups are mis-wired you won't get any humbucking effect (stand near an amp with a transformer in it and don't play, just wind the pups in and out and see if the hum reduces or increases with both pups on full ) and the sound will be weak.
Where it can go pear shaped is when people decide to mod an instrument without realising this and use two identical PUPS (e.g. two bridge pickups). Wired one way these will 'humbuck' but will sound weak, wired the other they will sound stronger together but hum will get worse with both of them dialled.
Thinking about it, if the bass has had its pups changed, is it possible this is what has been done?