For the same reason that it is called tuberculosis in English, from New Latin:
tuberculum + -osis
The term is a medical coinage of the 1830s (with the cognate first appearing in German medical publications). The English equivalent tubercle is a reference to the appearance of the lung tissue post mortem: white nodules, looking like tiny tubers, and with a pathological firmness.
This reference to nodules is the reason why 結核 was attached to this disease by the scientific community. The formation of such points in the lung tissue was adequately described by "the knotting of kernels". 結核 is also used in the field of geology for "nodule formation".
It must also be noted that the disease known both as 結核 and tuberculosis refers to various forms of infection by Mycobacterium tuberculosis, divided into pulmonary tuberculosis (肺結核) and extrapulmonary tuberculosis (肺外結核). In many of these, the tubercles are even more obvious, e.g. in scrofula (瘰) and osseous tuberculosis (骨結核).
Of course, throughout Eurasia there have been many other names for the various manifestations of tubercle bacillus infection throughout history. In Chinese, apart from 瘰, there are:
There were other interpretations of the symptoms of tuberculosis from traditional Chinese medicine, such as 骨蒸. On the other hand, the 19th century British medical missionary Benjamin Hobson used 肺癆病 as a new coinage alongside the translation + transliteration 肺體都比迦力 in his 1858 Medical Vocabulary in English and Chinese.
When Chinese diplomat 薛福成 Xuē Fúchéng reported on Koch's tuberculin therapy in 1890, he used 癆症:
The Berlin Doctor Koch has newly found a method of curing consumption using metallic residue to produce a drug that can kill "consumption worms" and is able to stop these worms from regenerating.
The history of the term 結核 actually goes back to Meiji-era Japan, where there was an appetite for Western germ theory expressed through kanji-based neologisms, and importantly an association of "consumption" with Western literary romanticism. From there the modern terminology came to be imported to China in the 1890s, with the increased opportunities for Chinese students to study medicine in Japan. There is an article from the 《亞東時報》 Yadong Times, a joint Japanese-Chinese monthly journal, dated to 1899, where the Japanese medical scholar 岡本武次 Takeji Okamoto entitles an article:
With the increased awareness of tuberculosis epidemics in Japan and China, alongside a desire for social reform and the impact of the 新文化運動 New Culture Movement, the term 結核 embedded itself into the national consciousness. However, 癆病 is used in 魯迅 Lu Xun's 1919 short story 《藥》, and as late as 1935 there is an advertisement for a Western medical treatment, "Kiazin", using 肺癆.