Yes, it will remove the -5% malus from Western Trade with an additional +1% global missionary strength bonus. After you enact this decision, an event will eventually fire where you have a choice of continuing the Sakoku Laws (or question them). If you continue to follow the Sakoku laws, you'll receive an additional +1% global missionary strength until the Emperor's death.
Also, once you border a Christian province, you can pass another decision called the Anti-Christian Edict that provides another +1% global missionary strength at the cost of +5% stability malus. If you get all of these going with Religious Ideas, then it's pretty easy to convert all of your provinces.