I would 100% knot. I don't think that it looks nicer to have them not knotted--in fact, I think it makes it look like they are cheap, imitation pearls, as I have never seen quality pearls just strung and not knotted.
Knotting pearls is also better in case the string breaks at any point (which does happen after awhile), the knotting will keep most of the pearls on the string, and you will only have to go searching for the two that fell off at the point where the string broke. If the strand were unknotted, all of the pearls would fall off, and you could definitely end up with some lost pearls.
Knotting also allows you to have a far more fluid necklace. If they are just strung without knotting, your necklace will either be too stiff (because they are strung very tightly) or it will end up with too much space between the final pearls and the clasp (because it wasn't strung tightly enough). When it is knotted, the knotting allows each pearl to kind of move on its own, but as part of the whole necklace. That is probably not the best way to put it, but since I make jewelry I have played around with this a lot, and that is definitely what I have noticed, and what other people I know have said as well.
I also agree with rosee that knotting the pearls keeps protects them from hitting each other constantly.
So I would say knot!