I know this thread is an old one, but I've also experienced the same (similar) problem importing products.
It seems to work fine with a small sample of products with short, simple names, but fails to allocate a category for each product when there are a lot of entries and longer product names. For example:
"product_name";"price_value";"price_currency_id";"categories"
"Sample Level 2 Award for Excellence - This is a longer product name [Text]";"0";"GBP";"12"
All the products follow a similar structure as above, and out of 50 entries only two or three entries are created in the "jos_hikashop_product_category" table (I fixed it by manually creating an SQL to add those entries.
However, there appear to be two issues:
1. Something in the import routine is failing to add entries in the product category table and crucially not reporting that back to the user and/or attempting to do anything about it
2. There is no way of viewing products that have, for whatever reason, been orphaned from a category, so it appears that although the import routine thinks it's successfully imported the products, they are not visible to the end user anywhere on the site (front or back-end).
As a programmer, I can see that there are many possible solutions, but the most useful one that I can think of (that would also be a good feature generally in my opinion): to add a filter for *all* products regardless of category, and a way to multi-select and (un)assign them a new category.
I'm not as pessimistic about HikaShop though, and overall it seems to be well structured and the responses to questions/problems I have seen have been swift and well considered, so I think this may be just an oversight.