I think any answers to these questions would be of necessity rather speculative until addressed somewhere officially...
I don't think they'll ever be addressed officially and with good reason. As you've seen, the implications can quickly become troubling. Even more so if cloning is involved.
... but I confess my thoughts went immediately to
Hank and Dean's "clone slugs" in Venture Brothers.
I read about Strephon's double - which was never described as being a clone, by the way - long before the wonderfully weird
Venture Brothers series ever aired but, yes, the story - and eventual fate - of Rusty's supply of Hank and Dean clones suggests all sorts of nastiness. Of course Strephon's double and Hank & Dean's clones aren't exactly analogous.
First, we only really know of
one double. A few faction leaders dismiss the appearance of the Real Strephon by remarking that Strephon had occasionally used doubles (note the plural) for various reasons, but those comments weren't made in an authorial voice; they're in-setting comments made by in-setting characters rather than metagame comments made by someone writing setting material. Putting it another way, the references to doubles is something which a fictional character thinks they know rather than an absolute fact.
Next, the double is never described as a clone. Now, we know cloning is possible; Norris cloned himself a daughter. We also know that genetic materials from Strephon are stored in various places; long after he was killed in the throne room Margaret in Delphi used such materials to give birth to twins naming Strephon as the father. Cloning is possible and should be an option, but we simply don't know.
Now I could have very well missed something, but I don't think we have ever been flatly told that Strephon had more than one double or had clones. He should have had more than one double and he should have had clones, but we've never been officially told. It's all just speculation on our part, well founded speculation, but speculation still.
Finally, the Venture Brothers clones feature a complete personality/memory transfer which again we've never been flatly told is possible in the
OTU. There are lots of hints, like the personality overlay device in
Mission to Zhodane or the late
MT adventure featuring a robot with a transplanting human brain among others, but nothing has ever been specifically laid out.
The Venture clones are kept in storage until the "active' Venture clones are killed whereupon the next set is decanted, memories/personalities transferred with some judicious editing, and the brothers live again. (Apparently, the process has happened so many times that Rusty and Brock have trouble remembering many copies they've decanted!)
If Strephon had a clone or clones and
if the 3I lacks the personality/memory transfer technology Rusty Venture uses, than Strephon's clone(s) must be already decanted and must be constantly briefed on the emperor's thinking and activities.
Like we've both said, things get really screwy really fast once once you begin walking down this particular road.
...but it's all hypotheticals, isn't it?
Exactly. Most of what we "know" is really just fan speculation. The actual published facts are remarkably few.