OK, this is quite a contentious issue.
One school of thought is that an upotted pickup has more 'air' or highs-it can breath more.
The other school is that it produces an unuseable squealing pickup.
My take is that an upotted pickup is bright but it's only of benefit at talking volume as anything over that and it becomes 'alive' and microphonic.
What we've discovered is that a properly potted coil, and by that I don't mean vacuum potted, one that spends along time in the hot wax actually ends up with a lower DC resistance and therefore has better clarity than and upotted/partially potted coil-also it doesn't squeal like a stuck pig PDT_040
What appears to happen is the heat from the hot wax anneals the wire and lowers the resistance-I've experimented with this alot and every time a potted pickup sounds better.
However , like I said, you'll find many staunch believers in unpotted pickups-I feel this is primarily because the early humbuckers that Gibson and several other makers made were never potted. I think that's a bit like fighting WWII with WWI weapons. things move on-modern amps for example have a lot more gain.
The statement that potted pickups are dull sounding is blatantly wrong-it's only the case with vacuum potting where the wire isn't heated and the whole process happens very quickly. A properly potted coil is not dull and in my experience sounds alot better.
The balance of paraffin to beeswax is important too. Beeswax is used to lower the melting point of paraffin wax but it's also alot more maliable and allows the coil to move.
So, a straight answer to your question-yes there is a difference in potted and unpotted pickups :D
