Solve product properties with custom taxonomies?

For each propery, ask yourself these questions:

  1. Is it likely that, on average, more than 1-2 posts will have the same value for this property?
  2. If so, do I need to filter posts based on this property, or is it just for display?

If you answered both with ‘yes’, then make it a taxonomy, otherwise a custom field.

Whichever you choose, you can make a custom metabox for that individual property, or several metaboxes that group related properties together. Whatever makes more sense.