I had a similar issue where Area 2Ds where lagging my game hard. The reason was because I was adding many Area 2Ds to the scene tree and removing them every physics update.
To solve the issue, I created a buffer of preloaded inactive Area2Ds, and whenever I wanted to add a new area, I would just copy over all the properties of Area 2D I wanted to add to the already-present-in-the-scene Area2D. The lag came from the engine having to look for collisions or something whenever an Area is added to the scene. Removing the area was as simple as just doing monitoring = false and monitorable = false