I don't want to speak for the developers intentions, but these are my thoughts:
The stock[M-1, M-2, etc.] ships are not meant to be made obsolete as they update themselves to the best M version available[and should be deleting the previous M version from the list].
You can't delete the most recent M version, as things like Ideology achievements are tied to your latest M version.
Now for player designed ships, an obsolete option makes sense. It will delete the ship from your list in the current game, but will re-insert the design as soon as the tech[actually before all the pre-requisite techs; seperate issue/bug] allows it to be created in your next play-through with that race/faction.
Note/Tip: If you don't use the M versions very often, you can select the "USER" tab in the ship yard and it'll move M versions to the very bottom of the ship list.
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Aside from that, if user made ships are re-inserting themselves onto your ship list after being made "Obsolete" within the same game, send a report. That shouldn't happen as far as I know.