Well if i remember correctly you need to run nautilus with:
nautilus --no-desktop --sm-disable
command to diasable the desktop loading. Although it really defeats the purpose of using WindowMaker if you gonna load huge, slow, and annoying Nautilus.
If you have gtk+2 i suggest Evidence, otherwise mc, rox, or xftree, or even xfm are good. There is a thread about file managers somewhere in here, seach for it to see what the most popular file managers are.
Ohh BTW, even Konqueror is faster than Nautilus.