Whenever a setting “disappears” from Notepad++'s preferences, try looking around the user-interface.

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Also, I and the rest of the npp-user-manual.org maintainers do our best to keep the manual up-to-date with the most recent Notepad++ version. The preferences doc gives a thorough description of each “page” of the Settings > Preferences dialog, and even tries to indicate when a given menu entry has been moved. If you search for “click” or “clickable”, you will quickly see where that option currently resides.

MISC Clickable Links is GONE! How can I turn off links now?

Whenever a setting “disappears” from Notepad++'s preferences, try looking around the user-interface.
Sometimes some cleanup and reorganization is done.
In this case it really was NOT all that hard to find where it moved to.