Is this single player? There’s a test you can do to see if this is the case then. What you are hypothesizing based on your observations with regards to animals and such going in stasis, is actually what is happening. Tascha was kind enough to give us the full details on it all back in October in this post.
As Tascha describes here, you can turn off the AI LOD with a command. If what you are observing is the source of your stutters, then in theory, turning off AI LOD would make it so those spikes would go away or lesson.