I don't really have a theory or headcanon to propose on the subject, but rather I was hoping that someone here might have something to offer on the subject.

Does anyone have any theories concerning Saturn and Pluto's relationship to one another in so far as their respective spheres of influence?

We really only get slight hints of it in the manga towards the end of Infinity and the beginning of the Dreams arc, but never really anything that is ever substantially fleshed out. Pharaoh 90 isn't quite destroyed, but rather is sealed away by both Saturn and Pluto within an alternate realm. Now, this struck me considering that Saturn's glaive isn't solely based upon that of the Grim Reaper but in reality the Ame no Nuboko of legend. This is important because it provides context for her role in both Silver Millennium, the present, and potentially Crystal Tokyo. Saturn's role is ultimately safeguarding the life of planets, stars.galaxies, and solar systems. We see some of that in the Dreams arc when she uses an astral orrery to observe and keep track of new and dying celestial bodies. So while Pluto keeps guard of time and space, Saturn keeps guard over their life and birth (I wonder what that means for Uranus and Neptune then. Hhhmmm...).

Likewise, it would seem that Uranus' theory held true, the only way to save Hotaru resulted in her dying and awakening Sailor Saturn, though that was not meant to come by the hands of the senshi, but by the daemon which used her body as its host.

The above said, what exactly was the relationship between Hotaru, Sailor Saturn, and Mistress 9 in her body?

Hotaru and Sailor Saturn only really encounter one another in Dreams (I'm still convinced that Sailor Saturn is unique amongst senshi. She doesn't have to necessarily awaken, and if anything could remain dormant.), and even then, she appears as someone distinct from Hotaru, and refers to herself as her guardian. 

Did Mistress 9 suppress Sailor Saturn within Hotaru's mind? I'm still confused as to how she was unaware of her presence. Why did Sailor Saturn allow Hotaru to become a host for Mistress 9? Why didn't she awaken when Hotaru was about to die in the fire? 

We have two very different things going on with Hotaru and Sailor Saturn. Saturn would be her past life/guardian, and Mistress 9 would be a daemon without a viable form who needed a host body in order to survive (That still doesn't quite answer what exactly Kaolinite and the Witches 5 were. If memory serves, they were perfected daemons who were able to take human form but weren't humans proper. Why then did Mistress 9 and Professor Tomoe's daemon continue to live in a host as opposed to acquiring perfected bodies of their own? Were Kaolinite and the Witches 5 human hosts who managed a perfect symbiotic relationship?). That being the case, all three parties would have been aware of one another. Hotaru in this life, a non-integrated Sailor Saturn from her past life, and Mistress 9 who was attempting to take possession of her body. How did they not come across each other? At least Sailor Saturn and Mistress 9? Shouldn't there have been a bit of a back story as to why it took her so long to awaken because Sailor Saturn had managed to lock her away or some such, and only now did she recall having encountered Saturn when she first tried to overtake Hotaru's body, but because of Hotaru's weakened state wasn't able to seal her away completely,because she was attempting to save Hotaru,thus granting her time to strengthen herself. It boggles my mind that Mistress 9 (or for that matter Kaolinite and Professor Tomoe) would't have been aware of Saturn's presence in Hotaru. I'm assuming that Saturn would have put up some form of resistance to being made a host by Mistress 9.

I theorized that after Sailor Saturn expelled Pharaoh 90 from Earth, she destroyed him and the Tau system, which would result in her death, and when Pluto closed the way into the system, she cut the Tau system off from the Sol system and the damage was limited to Tau.

I think Sailor Saturn really awakens when severe damage has been done to the system or Earth itself. Pharaoh 90, like the daimons, is a parasite who tried to take possession of Earth, infecting it. 

I think a lot of it might be speculation that Sailor Saturn might awaken if Hotaru continues to die. But the Outer senshi had to act on it because they didn't want to take any chances with Sailor Saturn. 

The reason Sailor Saturn allowed Mistress 9 to possess Hotaru is because she was still in slumber, while the planet wasn't in danger yet. I think that the Death Busters were somewhat aware that Hotaru had some power within her and that's why they chose her to become the host of Pharaoh 90's partner. And it probably took sometime for Mistress 9 to awaken because of the damage done to Hotaru's body. That's why Hotaru was being modified, not only was it to heal her but also to prep her body for Mistress 9.

As for daimons, in regards to Kaolinite, and the Witches 5, it was a symbiotic relation between them. There was no separate daimon possessing human. Professor Tomoe had grown obssessed with creating a better species of humans and he believed that perfect merging of human with daimon was the way to go.