@ronald, my apologies for reviving this old topic. You may have resolved this issue and moved on. But I just came across an old email notification about this, and though that maybe some of the new KM8 features could help.
You could export your list of Evernote Notebooks (using AppleScript) to a file. Then use the new KM8 Prompt With List action Action to pick the NB.
One limitation is that it will not show any items if the list if > 100. If that is what you want, then you could use MACRO: Spotlight Search Prompt by @DanThomas.
HTH.