Having links on these catalogs, even if they are low quality, is not always bad. People may find you, learn your company and become direct visitors of the website.
What it is bad, is that you only have links on these catalogs and nowhere else or the links ratio of bad vs good quality is too high.
If you have 10 good links and 1500 bad links (catalogue, aggregators etc), this will lead Google to determine that your website is bad quality and spam.
Good link would be an article that a blog/site wrote about your company and put a link to your website
If I were you I would not care about the automatic catalogues that automatically add my website.
What I suggest that you don't do, is go and register your website to hundreds or thousands of catalogues and provide link to them from your website. Don't register your website on catalogues where you expect to get zero hits or their content is inrelevant to your website.
Register your website manually on some specific catalogues that you expect to get some hits from there (at least one hit), or exchange some links with blogs or sites relevant to your company.
But dont do it too much.