The Cherwell Convention's Equipment Clause
I never said that the mere presence of security equipment constituted all [there] was to the equipment clause. To a great extent, it does do just that, since the equipment clause also assumes that if you have a "legitimate" requirement for those types of equipment, you will belong to a recognized interstellar government or police agency and have the documentation to prove it. If you don't have that sort of documentation, they don't give a damn how "legitimate" you were when you were built/outfitted. "You're equipped for slaving; you're a slaver; you're screwed. And if you don't like it, take it up with the Star Kingdom's lawyers. Lotsa luck. We're outta here." That's one reason that the Manties (and the Havenites) are two of the few star nations who rigidly enforce the equipment clause (even though they are 100% justified in doing so; see below); and one of the reasons a lot of Sollies are pissed off at them for doing so.
In fact, there have been occasions which a Manty warship has brought in a "security configured" ship which did have documentation, if the skipper of said warship felt there was good reason to believe the documentation was bogus. Sort of like a British captain seizing a US-flagged vessel off Africa in the 1820s because he believed the ship was flying false colors. If he was right, no sweat. If he was wrong, he could end up in a world of hurt. In the Manties' case, however, the skipper in question can be pretty sure he'll be defended in court by the SKM (which British captains could not always rely upon) and the number of instances in which the skipper in question turned out to be wrong can be counted on the fingers of one hand.
Ships with a legitmate requirement for these types of features are extraordinarily rare in the Honorverse. Unless you're StateSec, you generally don't need your own private hell planet as a place to park inconvenient numbers of prisoners. Just how big do you figure the penal population of most worlds is going to be? And why would it make more sense to load them on a specially outfitted starship and send them traipsing off across the galaxy to a prison rather than building yourself a nice, inescapable, suicide-charge-equiped orbital habitat out around Pluto somewhere? As for your other reasons for building such features into ships, I don't see most of them having any broad applications, either. Most star nations frown on forced colonization expeditions, for example. In fact, they are illegal under interstellar law (and have been for the better part of a thousand years), and the SKM does not recognize that as a legitimate reason for building in security features. For that matter, Manpower isn't the only source of slave traders in the entire galaxy. It's more common to see genetic slaves these days, but that doesn't mean there is no other version of the institution or that the Cherwell Convention applies solely to genetic slavers.
Military POWs are normally going to be transported aboard nationally-owned vessels and (supposedly, at least) under conditions laid down by the Deneb Accords. Large-scale transport of any other sort of prisoners -- as in large scale enough as to require cell blocks capable of securing hundreds or even thousands of prisoners aboard a special, purpose-built vessel -- is just about as common in the Honorverse as it is in the 21st-century Atlantic. That is, not very.