Hi Cesar, reducing the number of links per page is probably best practice. Google may decide not to index or follow all the links, or if the anchor text is very keyword driven it may be considered spammy. Pages with 1,000 links are probably passing on very little page rank at any rate,
I do understand your point about improving the user experience, but unfortunately algorithms probably won't understand the reasons behind this.
Is there a way that you can refine/restructure the results pages so that users don't see a very long list of results/links? E.g. for a page that has 1,000 results, could you paginate according to letters of the alphabet?
1. It could possibly help you. There's no penalty for having too many links per page (unless they appear spammy), but some restructuring could ensure that internal links pass on more link juice.
2. If these pages are not linked to from elsewhere, they probably will see a drop in ranking/page authority.
Good luck!