Well, I have always got taxonomy to work with node_import 5.x-1.6.

The taxonomy term should be a column in the csv file, and I map this to "Taxonomy: Catalog" during the import.

Multiple terms can be separated by pipe "|" sign in a csv file, assuming your fields are comma separated e.g. assuming you had products that could be classified as Term1 & Term2, then in the Taxonomy field you should have:

.....,"Term1|Term2",...., [see the readme.txt file unde modules/node_import]

I am running Taxonomy 5.7. & Taxonomy Menu 5.x-1.03 with drupal 5.7

So the only outstanding things for me are:
1. Image imports with node_import 5.x-1.6 [I have not had another go at the patch...]

2. Speed - see my support request on:
http://drupal.org/node/270584