With the additional side question of “how many hypomeiones are you going to have to funnel through therapy programs”?
Yeah, that’s a bit of a different issue. After all, in ad/an situations generally you get the whole polity as part of the deal, and so you can’t really pull an “except those assholes”. Or if you do, it’s something you sort out in the early stages such that as part of this deal, your asshole secessionist movement gets to be seceded, belike.
Suffice it to say that if y’all have an asshole problem that would require fences and sentry guns, y’all or at least that chunk of y’all don’t get to be admitted, or even annexed. The best you can hope for is the kind of satrapy more accurately described as “involuntary protectorate”, in which case you get to be policed in detail by surveillance dust and security drones from the Bitterness-class involuntary protectorate enforcer orbiting 'way overhead, and may very rarely even see an actual Imperial unless Admiral Cluster Bomb is feeling chatty.
So what is this status intended for?
Well, it’s to deal with those admissions and annexations where they’re happy to take the polity, but there are those certain minority sections of society which while not in themselves a violent insurrection are nonetheless insistent that the Wehrmacht/IJA Did Nothing Wrong, or our contemporary Team War Crimes & Genocide Are Perfectly Fine When Our Side Do Them.
(I mean, on the one hand, the galaxy would probably be a better place if they all spontaneously dropped dead tomorrow, but, y’know, ethics.)
And its practical effects?
Well, they can’t deport you simply for being a hypomeion. After all, having admitted or annexed your former polity does rather concede your right to live in it.
(That said: when a citizen-shareholder commits a felony, having thus grossly violated the responsibilities of citizen-shareholdership, per the Charter, they lose said citizen-shareholdership, becoming a resident with a -D “disenfranchised” SI, although able to maintain Imperial domicile.
But that can only apply to citizen-shareholders, since you can’t take away from people what they don’t have. Resident non-citizen-shareholders - be they the mainstream of domiciled or transient -R "resident"s without other qualification, or one of the other non-minor resident categories [disenfranchised, incapable, proscriptee, metic, or hypomeion] are thus deported as personae non gratae under the circumstances. So it does lower the threshold at which the Empire will declare that it is officially done with hosting your bullshit.)
In terms of actual civic rights inaccessible to hypomeiones: well, the aspects of those which recapitulate in more wordy forms fundamental rights can’t be taken away anyway, and while in theory there are things they could clamp down on in re speech, assembly, association, travel, etc. - see article IV here, and remember that any such clamping down can’t violate the fundamental rights - in practice is is extremely disinclined to do so. The power exists, but using it in anything except the most extreme circumstances would be a profound violation of Imperial values that wouldn’t be accepted by, well, anyone. I don’t think it’s ever happened, and if it did, it was only at the margins.
There are two notable exceptions here.
One is the right of arms, which bearing in mind Imperial culture in general is about as blunt and symbolically visible a statement of “you are not worthy of admission into our circle of trust” as you might imagine.
(The primary effect of this is social, as you might imagine, because it makes what the Empire as a collective of citizen-shareholders thinks of you real clear even to people who didn’t notice the -H tag at the end of your SI.)
The other relevant one is article XIV, rights of genesis, because as you may recall the Empire doesn’t consider reproduction an unlimited right insofar as it necessarily involves someone else, even if reproduction for your species is just sparkling mitosis.
As mentioned, the powers granted by the fifth amendment that added article XIV permit the regulation of reproduction where matters of public health and child welfare were concerned, and the same factors which make people hypomeiones rather than metics qualify pretty well as “unfit parents, unfit circumstances” by the standards of the Reproductive Statutes.
So, to sum up, its essential effect is to apply the weight of social opprobrium to you until you either get your act together, get out (of your own will, and not letting the door hit you on the ass on your way), or get dead. Any of the above is acceptable.