RAW with a Ninja 1//rogue 1 gestalt you would get both sudden strike and sneak attack, they are different class features and you would get them both, however RAW a Rogue 1//Spellthief 1 Gestalt would only have sneak attack 1d6 since the same class feature cannot be gained from both classes at the same level.

The way I avoid this problem, and the simplest answer is not to play gestalt, but thats obviously not helpful since you are asking about playing gestalt. So, if you wanted to go Rogue//Spellthief go rogue//fighter at 1st level and then multiclass into Rogue//Spellthief at second.