Only the high-level ones. Perhaps allow missions to give 1-2 million credits. This would give less need for trading. I know I would mostly give up on trading if this was implemented. Doing 100 missions for a BS? Sure. 25 for a gunboat? Sure!
However, this would mean that some houses would need to be allowed higher mission levels. For example, Rheinland should have missions (HARD MISSIONS, either swarms of enemies, or battleships/cruisers) worth 1 million credits. I would almost never trade again!