Duplicates are allowed. What you probably want to achieve is that certain duplicates are not removed or not listed. Both can be done in recent versions:

1. If your duplicates are all within one folder, you can e.g. unmark all bookmarks from that folder: Choose the folder from "-- Select a folder ..." to get the corresponding unmark button.

2. To not list the bookmarks in the first place, you have to use “expert mode”. Switch all default rules to “off” (or delete them), and create a new “filter” rule. Into "Name matches" of that rule you can insert e.g. "\0Frequently used\0" if all your duplicates which you want to ignore are contained in folder(s) named “Frequently used”. You can specify your desired exceptions much more fine-grained (using regular expressions for the full path of the rules). To preserve your setting, you have to store it (locally or remotely).

Actually, the default rules in “Expert mode” already contain an example of a “filter” rule with “typical” names for such folders.