I have the same issue, hence Googling and finding this.
My feeling is WP’s own “Link Manager” was depreciated because it was non-standard.
My approach is to install it for inspiration on the object design, and then use the “CPT UI” plugin to reproduce it as a Custom Post Type & Custom Taxonomy.
Maybe 30 minutes work, no code tinkering, and then you own your own Links custom object fully compatible with ACF.
Therefore achieving the same thing but without relying on any ACF mods.
Hope that helps.
