Safari removes only bad cookies!

See this article Manage cookies and website data in Safari on Mac - Apple Support

You can also click on History on top menu bar > click on clear history a pop up appears .Choose clear all history from drop down arrows and click on clear history , this will delete all past browsed history and cookies , but if you want history to be saved only cookies are to be deleted then you have to hold option key then follow the same process .And some users enter in user library click on safari > find folders local storage and database and delete the contents of it in the trash , restart the Mac and empty the trash , but this is not a permanent solution once again you browse the caches , cookies will get developed in a normal browsing mode , to avoid saving the web site data some users use private browsing mode in which cookies are never saved .And to view a website cookies are essential .

The databases are stored in ~/Library/Safari/Databases that you can delete. Others may be Forever cookies which will always repopulate.

EDIT: Did I mention that deleting cookies is pretty much a futile effort?

Read this article Safari for Mac: Databases stored on your computer using Safari

You can clear all history and web site data , this will remove each of it , if you enter ~/Library/Safari and delete entire contents of safari into the trash all folders of that will be deleted , when Mac is restarted and the trash is emptied all folders like database and local storage and other folders will be recreated .

As you never deleted or avoided deleting the history and website data from months this will happen , see this article Clear your browsing history in Safari on Mac - Apple Support

If 68 cookies are still stored remove them once more .

But as I told you this is a temporarily solution in normal browsing , you browse the sites they are ought to be saved , only prevention is delete them on daily basis ( as it is optional ) or switch to private browsing Browse in private in Safari on Mac - Apple Support and some like to save data for references , and like to view previous links in history or whatever .

No, that's not a feature. It may be because when you choose to delete cookies when you click "Remove All" it will take some time to delete all of them. The window will repopulate before it's finished removing everything, so let it take a moment or two to finish.

Also, cookies and website data will be re-populated from other sources like Top Sites, Quick Website Searches, Search Engine Suggestions, Top Hits and others.

You can experiment what Mac jack suggested is to be followed as there is lot of website data stored and it clicking on removing all website data from safari preferences could take some time to delete all of it .

Saving lot of website data is to be avoided , some users like to save it , but it should be cleared frequently.

Safari/Browsers – can’t delete cookies

Evercookie

The myth of the dangerous cookie