Honestly, OP, while I'm sure that generalizations can be made it's kinda like tonewood - there are so many variables that it's hard to say with real conclusivity. There are different ways to shape a magnet, different ways to wind the coils (different gauges of wire, too) different sizes of polepieces etc...
Would an ALNiCO pickup sound different from a ferrite ceramic one? Yeah probably, but two different alnico pickups would sound different from each other too. I've got a jazz with dimarzio model J pickups in it, and honestly - it sounds great. Couldn't even tell you what magnets they've got.
Would a guitar made of alder sound different from one made of ash? Yeah probably, but so does two alder guitars. Heck, grab a strat made from a single piece of decades old air-dried alder from an old-growth forest and compare it to one made of sixteen pieces of some cheaper kiln-dried stuff and it'll also sound different I'm sure.
Would an ALNiCO pickup sound different from a ferrite ceramic one? Yeah probably, but two different alnico pickups would sound different from each other too. I've got a jazz with dimarzio model J pickups in it, and honestly - it sounds great. Couldn't even tell you what magnets they've got.
Would a guitar made of alder sound different from one made of ash? Yeah probably, but so does two alder guitars. Heck, grab a strat made from a single piece of decades old air-dried alder from an old-growth forest and compare it to one made of sixteen pieces of some cheaper kiln-dried stuff and it'll also sound different I'm sure.