How is better to store at DB 1-side relationsip from CPT to many Taxonomies Terms ID’s?

If I am understanding right, you’re suggesting creating separate database tables both for your post type and taxonomies. You don’t really need to do that at all. Just create a custom post type which WordPress will store in the {prefix}_posts table, and create a custom taxonomy for that post type which WordPress will also handle in its native tables. It’s all built in already, no need for custom tables, and that’s how taxonomy terms are meant to be assigned – when you’re in a CPT you can assign it some terms, but in the terms themselves you don’t assign to a CPT.