You mean P90's with rod magnets, and not just inert slugs instead of the screw poles?
Think to a Firebird PU vs a mini-humbucker: vertical magnets favor touch sensitivity and a brighter tone, a bit thinner (unless they are strongly magnetized, in which case they might favor bass frequencies too). Horizontal magnets laid under the coil(s) contribute to a warmer sound, less focused, more compressed, with a wee bit slower attack.
All other things being equal, of course (I mean: with the same kinds of coils, pots and so on)..