Yep, makes no sense whatsoever. I've read a few novels involving contemporary humans getting access to advanced space propulsion and converting modern in-service submarines for space. In all cases it was an expediency move made immediately after acquiring the new technology and before purpose-built hulls could be designed and built. Like in Space Battleship Yamato/Star Blazers, it was a desperation situation, defending against alien invasion or scouting for where aliens who had attacked may be located. But it made sense as a temporary stopgap - pressure hull, life support, nuclear reactor aboard already, etc.

That is quite different from Yamato, which was a 150 year old sunken wreck of a surface vessel. Surely other preserved ships would be better candidates. Or leveraging existing submarine manufacturing facilities. It was awesome to watch as a little kid, and the relatively-recent live action movie was pretty cool.