The why of the matter is unresolved. Some suppose that crime serves as an alternative following failure in the job market induced by these characteristics. Others suggest that there is bias in the criminal justice system. But, there is evidence that people who are convicted of crimes are disproportionately short, fat, and ugly.
These factors apparently exist at statistically significant levels, presumably even after controlling for the major impacts of race and gender on crime and criminal justice outcomes. I've only glanced at the underlying research and also haven't determined if there were controls for poverty and education, or if the impacts are similar in all demographics and in all types of crimes.
My strong suspicion is that the study referred to in the link is simply an operationalization of long known associations between social class, crime and the criminal justice system that have been a relatively minor aspect of criminology in American society. In the wake of the Civil Rights movement (and a long national legacy of racial politics), American academic research has focused instead of the identity politics of race, identity and gender, more than the closely kindred, but mushier issues of social class. But, observations about social class that have often have associations with propensity to commit crimes as an element of them, far predate the modern social sciences and are probably older than history itself.
Short stature and obesity have strong links to poverty (most researchers presume that this a function of poor childhood diet), and any appearance associated with poverty (or for that matter any other undesirable social category) becomes, almost by definition, unattractive.
A link between low IQ (regardless of whether the source is genetic or environmental) and a propensity to commit crimes and to receive disproportionately serious treatment in the criminal justice system, is well established. There have been some indications in research into IQ that the "g factor" (i.e. non-test specific element of IQ) may be linked at a statistically significant level not just to mental fitness, but to general biological fitness (life just isn't fair, is it?) even by measures as imperceptible as sperm count and sperm imperfections. So, some differences in appearance may be part of a total package in which low IQ is the main factor driving the crime and criminal justice outcomes.
John T. Molloy, whose book "Dress for Success" (1975) made a case for the economic advantages of dressing like a member of the upper middle class that was the sartorial bible when I was in the job market, also wrote the less well known sequel "Live For Success" (1981). "Live For Success" extended his advice on what to wear in order to infiltrate the upper middle class to other aspects of superficial appearance that are part of the upper middle class identity like obesity, posture, table manners and speaking style. Paul Fussell's book "Class" makes similar observations from a less scientific orientation.
Molloy's account is while acknowledging class distinctions that Americans committed to the notion that all men are created equal are uncomfortable acknowledging is also ultimately a hopeful one. In his view, it is possible for anyone (or at least most people) to socially adopt the most important aspects of the upper middle class person. Birth, in his view, is not fate; just a helpful or not so helpful legacy that can be overcome.
His recognition of deep seated cultural aspects of social class, that can be adopted with extraordinary effort, as key to success as our society defines it is also IMHO (possibly independently reached), one of the core factors behind the sucess of academic approaches like those taken by those few educational programs like KIPP and the Denver School of Science and Technology that have had a widespread, consistent track record of securing high academic achievement from low income students.
This is still an uncomfortable conclusion. The linked study on crime and appearance, Molloy's research, and the approach of some of the most successful academic institutions all point to the notion that one of the keys to both success and to avoiding social failure is to profoundly change your personal social class identity and many of the internalized cultural elements that make you who you are as a person, if you are born into a lower social class. In this view there is some truth to the "Oreo" and "Twinkie" taunts, that minority social climbers must be "white on the inside" to some extent to achieve social and economic success, and Ataturk wasn't completely off base in 1925-1934 when he insisted that Turks adopt not just Western political and scientific innovations, but Western fashion, as he tried to bring Turkey into the modern era, despite the absurdity of having Turks wear clothes designed for a much cooler Northern clime. The price of success may very well be your soul, at least if you are not fortunate enough to be born to privilege. Needless to say, this is a high price to pay for academic and economic success.