You're correct that the odds of the enemy capturing, repairing and returning to service captured enemy vessels during WWII was slim. Unlike ships during the age of sail, most naval vessels of the era required an incredible amount of knowledge and training to operate effectively. In addition, unlike sailing ships, ships of this era required thousands if not hundreds of thousands of moving parts to keep the ship operable, and it's not entirely easy to get spares for a ship that you did not design or build. I'm not saying that it couldn't be done (or that it wasn't, Japan, Germany and the UK all captured numerous vessels of enemy nations throughout the war), but more often than not, it's wouldn't have been worth the effort.

To answer your question though, a key reason why ships were scuttled or purposely sunk was for security and intelligence reasons. When a ship was typically evacuated because she was lost for whatever reason (battle, weather, imminent enemy capture), crews would make the effort to either destroy or take with them cryptography equipment as well as code books, war diaries, maps, etc. Despite this, an enemy salvaging party if given the chance would absolutely work to save an enemy ship if given the chance. For one, being able to physically inspect and understand how the enemy constructed their ships would be a huge intelligence boon. For another, think of a ship as a floating base. Being able to get a look at (even if things are destroyed or unrecognizable) the ship's stores, crew quarters, etc. could give intelligence analysts a huge amount of useful information on how the enemy is conducting their war, the average age or service length of the crew (which could help pinpoint how effective or hastened their training pipeline is), and so on.

Now as far as examples where ships were captured, and returned to service under the capturing navies flags, there are a few that come to mind. Germany was able to capture at least one British submarine (HMS Seal) and return it to service. Japan was able to capture multiple destroyers and gunboats from the U.S. and British navies. However the majority of these captured ships did not see much service after their capture and were typically relegated to use as training ships.