How to harvest peppers and tomatoes for later use in sauces without harming taste
We've been freezing both vegetables for years, with no loss of flavor.
Tomatoes
Unless your tomatoes have very thin skins, I recommend that you skin them prior to freezing. If you don't remove the skins first, you may wind up with the leathery skins floating in your sauce, which isn't really appetizing. To easily skin a tomato, press the back of a sharp knife onto the tomato, press gently, then rub the fruit to loosen the peel. Next, just make a small cut and start peeling with the sharp side of the knife. We also remove all seeds at that time. Alternatively, use a food mill (not a food processor) to process the tomatoes.
We freeze the tomatoes in roughly one-quart amounts, which is what we generally use at any one time.
Peppers
As you noted, you'll cut the peppers in half and remove the seeds, but we've found with experience that the frozen peppers, when thawed, turn mushy; we get around this by using the peppers as soon as we remove them from the freezer. They even retain a little crunch!
We freeze our peppers by cutting them into edible-sized slices (after removing the seeds), laying them out on a cookie sheet, and then putting the entire sheet into the freezer for a couple/three hours. This helps the slices to freeze faster (which we assume helps keep them move flavorful, but that's an assumption only); it also keeps them from sticking together after we bag them. When the slices are frozen, we bag them. We then use only the number of slices we need for a dish, cutting them up immediately upon removal from the freezer bag and adding to the dish mostly frozen to avoid the yucky mushiness.
Given that thawed peppers are really not appetizing, I don't know if you'll like the end results after smoking them. They will definitely NOT hold any kind of crunch and may even somewhat disintegrate in your sauces. Well worth a try to do it, though, especially if you do only a small test batch first.