Good question. Zero difference in sound between wood and plastic -- at least not any that we have ever heard.
As for holes / no holes, we prefer to have exposed pole pieces whenever possible and believe that the instruments experience slightly better tone by so doing which is why all of the Standards come that way and why left to our own devices we will spend the extra 20-30 minutes drilling holes in our wooden covers even though we charge the same price with or without holes.
That said, there are two very big caveats...
1. If you dig in so hard that you have a tendency to brush against the poles with your picking hand. This will cause noise and for players like that (Joey, by way of example), we recommend solid covers.
2. If you tend to sweat a lot because your sweat can rust the pole pieces.
Like everything else in building instruments, it is all a question of choosing the right trade-offs and nothing is perfect for everyone. As a guy with a light touch and who does not sweat much, all of my basses have exposed pole pieces...
Hope that helps!
J