The Emergency Off or EMO button is more forgiving. It simply cuts off the primary power supply and leaving the ship's circuits deadish! However, crew can then manually reset the button to allow current to flow through again. There is nothing lost but time.
If the Crew can reset this button, then so can an attacker. If he can't figure it out himself, he can always capture fleeing crew members and "persuade" them to give him the information on how to reset the button.
There are a few reasons to destroy a craft. The first and foremost reason is to protect secrets - both data contained within the data storages on the ship, as well as technological data. If you can get your hands on a brand new F-35 it would be awesome.
It could be that up until know, humanity was either alone and they have found a new enemy, or humanity was united before and now there are factions. Self destruct was not neccessary because there was no enemy from which to hide data/technology. Now there is. Self-destructs become mandatory for all new ships, and old ones must be retrofitted within the next X months.
Maybe it becomes illegal to completely shut off the ship because that way it would be too easy to board (automated defenses are now required, and they need to be powered). This means ships that become retrofitted with the self-destruct also get fitted with automated defensed, and a complete shutdown is not longer possible because power generation must stay on, as well as targeting systems, a rudimentary attitude control, and the automated defenses.
Maybe the retrofiiting process takes longer then required, and some ships can avoid getting retrofitted for years. This would be ample time for a storyline with both types of ships to happen.