have you passed one turn after the surrender?  To make it "effective", you need to change turn, so then you'll get a message saying they were exterminated.

They may have ships left, and my guess is they are "under" one of the planets. When a faction swaps because of influence or surrender, any ships that were on the planet rarely move out from under that planet.

You can turn off the option "Fight to the last ship" or whatever its called in options under custom game.

As long as a civ has like 1 ship left, they are consired still in it to win it.

Also, there is sometimes a bug that flags "Pirates" from a Starbase, Shipyard etc as being from the previous race, and you need to kill the pirates.

Step 1:  Build the Hyperion Planet Jump Drive

Step 2:  Start up the Planet Core Engines

Step 3:  Hyperspace Jump to a nearby star system

Step 4:  Kill the bastards under the planet