I don't see any possible evolutionary disadvantage in situs inversus(the condition where major organs are mirrored from their normal positions) when people with situs inversus can have a normal healthy life.
In the Wikipedia article linked to in the question, one will note that there are several medical conditions associated with situs inversus, including congenital heart disease, primary ciliary dyskinesia, and Kartagener Syndrome. These can easily lead to reduced fitness for reproduction, especially PCD/Kartagener Syndrome, as one effect is male infertility due to lack of functional cilia on sperm.
Therefore, there likely is a negative pressure on the alleles responsible for this condition, explaining why it is so rare.
If a polymorphism is neutral and has no effect on reproduction, it will not necessarily present itself to the population in a 1:1 ratio. For instance, for a single-gene polymorphism with two alleles in the absence of evolutionary forces like selection and gene flow, the trait will be at Hardy-Weinberg equilibrium, meaning the two different alleles will be present in some ratio (not necessarily 1:1) and will stay in that ratio from generation to generation. Of course, I'm not an expert on animal physiology and I don't know the genetic basis for situs inversus, but either way two equally fit traits may still be present in the population at very different ratios as there is no force pushing them to be present at equal ratios.
Traits undergoing density-dependent selection, on the other hand, such as sex, are under selective pressure to exist in a 1:1 ratio. There are unlikely to be any such forces acting on situs inversus vs situs solitus
I am an eighty year old woman with Kartageners Syndrome. This means, I have bronchiectasis which was diagnosed in 1948. The disease was isolated in my left bottom lobe. I also have chronic sinusitis. I think cilia is lacking or if not lacking at least too short to be effective. For most of my childhood I was unwell but after age eighteen I seemed to be quite a bit better and I have lived a healthy life. It is only recently that I have had health problems relating to Kartageners and I tend to think my age is now contributing to lung infections and therefore the quality of my life is deteriorating.