Hi!
Thank you for the details, I think I know what the problem is.
The product variation permalinks are indeed incorrect. I have debugged the code section, which gets these permalinks, and I found, that WooCommerce is not active on the main site there. The product variation permalinks need to be requested from WooCommerce, however the request is made via the site where the search is currently running on (main site). Unfortunately this is not possible to resolve from the plugins perspective.
I recommend one of these 2 possible solutions:
1. Either remove the product variation filter/post type from search
2. Or Network activate WooCommerce, to be able to resolve the permalinks on the main site as well.
Personally, I recommend solution 1. if the variations are not so importand in the live results list.