Yes, it happened to me too for the last few months. Can't recall the exact date or version number though. But I have confirmed that this has been fixed.
The version I just checked is Sequoia 15.5 with Pages/Numbers 14.3 (7042.0.76).
Two types of verification done:
1) Creating new document, entering some data and save it.
2) Modifying existing document and save it.
The location of the file doesn't matter, be it locally or residing in iCloud Drive.
Unfortunately, whatever files that had been amended/created during those "problematic" period will still have the extension shown regardless of your settings. For these, you have to manually remove the extension one by one.
Clarification
The file extension has always been there since early days. It is just that it is hidden and behave in line with user's expectation. But somehow, for the last few months (can't recall the exact date range or version number range), there were bugs either at the system level or the app level that causes the inconsistent behaviour. During that period, Pages/Numbers app no longer honoured the settings set at the Finder. Personally, I'm glad that this has been fixed, but kind of annoyed that we have to waste time fixing "the mistakes" made by the developers.