The quote you have provided comes from the first of the light novels, which take place on July 19.
It was July 19th.
The fault lay in that date. Because summer vacation would start the next day...
The Railgun version of the Sisters arc extends from August 10 to August 22, according to the wiki.
So Misaka had heard rumours about the Sisters for weeks, at least, before coming face-to-face with one.
The full version of your quote goes:
“Hah. Don’t make me laugh. What is all this about the ‘brain of god’? Have you heard about the supposed military Sisters created based on an analysis of my DNA map? It seems to me these lucrative side effects are more important than that objective.”
If you read the Railgun manga version of that encounter, you will see that Misaka has an expression on her face like 'Really? People actually believe that?'
Given how distressed she was when she found out the Sisters were real, I think it is safe to assume this was a rumour that she heard but dismissed as ridiculous.
Considering that the Sisters had been operating outside for some time, it is hardly inconceivable that rumours of their existence had sprouted.
EDIT: Rereading the third novel led me to this quote:
However, recently there had been a rumor spreading throughout Academy City that her DNA map had been used to create military Sisters. It wasn’t that rare an occurrence. Mikoto was one of the seven Level 5s and a scholarship student at the prestigious powers development school of
Tokiwadai Middle School. There had been countless baseless rumors like that about her. That was why she had not believed the rumor.
Or perhaps she had simply not wanted to believe it.