Quote: "So, what's the consensus for id tracking?"
No real consensus I guess. You can treat them manually or let some kind of automatic function to find a free id and have it assigned for you.
If done manually you may have more control with z-rendering priority, but it requieres more work and planning.
In any case it is always better to keep id numbers as low as possible. Try to avoid high id values.
Quote: "Are Particle Systems considered a 3D Object"
No, in-built particles have their own id set.
Quote: "What about textures & fx? Do they share?"
No