I can't find any explanation of how the weapon works in the book, and I note that Wikipedia agrees with me. Given this, it's hard to make any meaningful comments on the physical plausibility of the technology. However there are some interesting points to make.
The weapon obviously tinkers with the geometry of spacetime (i.e. the metric). In chapter 22 of Absolution Gap we find:
There was no inertial protection against that acceleration, even though bulk control of inertia had been within the reach of Conjoiner technology for more than half a century. It
couldn’t be allowed. The other technology that the ship carried—the glittering, tinsel-like machinery of the hypometric weapon—was highly intolerant of alterations to the local metric. The hypometric weapons were difficult enough to use in nearly flat, unmolested space-time. But within the influence of inertial technology they became malevolently unpredictable, like spiteful imps.
and in chapter 34 of Absolution Gap:
Scorpio’s thoughts drifted to the hypometric weapon moving in its shaft, a corkscrewing, meshing, interweaving gyre of myriad silver blades. Even immobile, the weapon had felt subtly wrong, a discordant presence in the ship. It was like a picture of an impossible solid, one of those warped triangles or ever-rising staircases; a thing that looked plausible enough at first glance but which on closer inspection produced the effect of a knife twisting in a particular part of the brain—an area responsible for handling representations of the external universe, ah area that handled the mechanics of what did and didn’t work. Moving, it was worse. Scorpio could barely look at the threshing, squirming complexity of the operational weapon. Somewhere within that locus of shining motion,
there was a point or region where something sordid was being done to the basic fabric of space-time. It was being abused.
In general relativity the structure of spacetime is related to the stress-energy tensor, which in most cases you can think of as the amount of matter present. For the interesting stuff like wormholes and FTL drives we require exotic matter, which as far as we know does not exist. General relativity is a local theory i.e. it tells you how spacetime responds to the local value of the stress-energy tensor. To create an effect remotely, as the hypometric weapon does, you would need to change the stress-energy tensor at the remote location i.e. create some (exotic) matter there. There is no suggestion in the book that the hypometric weapon does this. I think we have to assume it's using some property of spacetime not described by general relativity or any other currently known physics.
On a side issue, the comics Tales of the Jedi came out before Absolution Gap and Wikipedia informs me they describe a weapon called the Null sphere very similar to the hypometric weapon. They even use the phrase weakly acausal to describe this type of weapon - a phrase that Reynolds also uses. Since I know nothing of this series beyond what Wikipedia tells me I won't comment further!