If the effect of the Diseases are visible, then the glass dome could provide an extremely good sexual selection tool, and the species would evolve to consider it attractive - if you want, even the 'glass top' itself could be natural to the species (Although it probably wouldn't be actual glass in that case*).
This is similar to how humans have come to evaluate symmetric faces as attractive; asymmetric facial features correlate with diseases and other genetic issues. Symmetric features then suggest a lack of such diseases.
If such brain diseases are common, and have been so for a long time, then being able to select partners without such diseases would be a strong evolutionary pressure.
Humans - and most other creatures on earth have evolved thick skulls because that helps protect our brains, which increases longevity and thus increases the probability we will have children. With your species, all you need is for the diseases to be a higher evolutionary risk factor than damaging their brain through physical force -- and evolution will have done the rest.
*In this case, the species might have evolved somewhat transparent skulls, and considered being able to see brains clearly as highly attractive. And as a result, replacing the top of their somewhat transparent skulls with completely transparent glass could be common practice.
Some of the older answers have elements of this answer - but I realised they combined very nicely, and wanted to post an answer that pointed that out - hopefully clearly.