In a bowl, whisk together the soy sauce, Dijon mustard, honey, and black pepper until well combined. This marinade will add a delicious balance of salty, sweet, and tangy flavors to the skewers.
Place the salmon chunks in a shallow dish. Pour the marinade over the salmon and ensure it's evenly coated. Seal the bag or cover the dish and refrigerate for at least 20 minutes to allow the flavors to meld.
Preheat your oven to 375°F (190°C).
Thread the marinated salmon chunks, cherry tomatoes, and lemon slices onto the soaked wooden skewers alternately.
Place the skewers on a baking dish lined with parchment and bake in the preheated oven for about 12-15 minutes, or until the salmon flakes easily with a fork and the cherry tomatoes have softened and begun to blister.
Carefully remove the skewers from the oven. The lemon slices may have caramelized slightly, adding extra flavor. Serve the baked salmon skewers hot, garnished with fresh herbs like parsley or dill, if desired.