I'd like to make a few points on this matter. Firstly, even if her face isn't known by everyone in Academy City, many people do recognize Misaka Mikoto. Secondly, Academy City has the motivation and the means to keep Misaka's fame level down. These points are partially in conflict since I'm arguing on one hand that Misaka is famous, but on the other hand I'm saying she isn't. I don't think these points are irreconcilable, but my goal here is mostly just to present evidence and analysis from the light novels and manga rather than to reconcile the two points.
In the first novel, Mikoto says this on pages 6-7:
Hey, have you heard? They're developing some military-grade little 'sisters' for me, based on my DNA, that they can use in the army. I guess the by-products were sweeter than the ultimate goal, huh?
The Railgun manga and other works in the franchise expand on this comment, explaining that it is a rumor Mikoto has heard. Since we know from later works in the series that this rumor is actually true, it is probable that it was started (or at least helped along) by mysterious sightings of look-alikes of Mikoto Misaka. In this case, people would have to have an idea of what she looks like. The Tokiwadai uniform obviously helps a great deal at identifying her.
Now, there are some possible reasons that Mikoto Misaka wouldn't have celebrity status. First off, Academy City is a very secretive place, and Mikoto Misaka is an invaluable research subject. Touma Kamijou comments several times on how secretive and stingy the place is in protecting the secrets of its curriculum, including in volume 4 on page 2:
Plus in consideration of its own secrets, as well as the potential threat of student kidnappings (read: theft of test samples), Academy City stubbornly disliked allowing its students outside of its walls. Gaining permission to leave required three written applications, the implanting of microscopic devices in your bloodstream, and the arrangement of a legal guardian...
So, Academy City is very secretive and might prefer to keep their top espers out of the public spotlight. They have the means to do so, too. The very reason Touma is on vacation at the beach in the fourth volume is so that the some information control can be done regarding his recent activities:
The upper echelons of Academy City were the ones most bothered by the commotion. They said to him, "Hey, hey, Mr. Kamijou. We'll fix this up with our information control, so go away somewhere you won't cause needless chaos, stupid."
So, from these passages from the fourth novel, we know that Academy City is very secretive and that it has great influence over the information released inside and outside the city with regards to their research.
Lastly, volume 7 of the Railgun manga has a great deal to say on this issue. Chapter 43: Negotiation partly chronicles the attempts of a committee to find a public representative for the Daihasei Festival from among the level 5 espers and they mention that the Daihasei Festival will be broadcast to the world. The committee tries to get Mikoto Misaka as the representative, hailing her as "the most normal level 5". When the committee representative speaks to the headmaster of Tokiwadai, the representative comments on Misaka's past experience performing demonstrations in Russia. The headmaster refuses the committee member's request. The headmaster's reasoning is explained in thoughts and flashbacks: Based on previous incidents, the headmaster thinks putting Misaka into the limelight isn't good for her. In the flashbacks, we see these three phone calls:
"I witnessed your Misaka kicking the vending machine."
"A person resembling Misaka was chasing a high school boy!"
"A person I believe to be Misaka-san was playing some sort of survival game in the backstreets."
Once again, these phone calls show that Mikoto is recognized by some people. This isn't the only point I'm trying to make here, however. The headmaster believes the public spotlight has had negative effects on Mikoto, and has been trying to keep her away from it. This attempt to get her away from the media could be a reason she isn't widely recognized. Without constant attention from the media, many people could start to forget what she looks like.
My conclusions are that Misaka is more widely recognized than the question indicates, but at the same time, Academy City is likely to be suppressing Misaka's fame because she is a valuable test subject and they vigilantly guard the secrets of their curriculum, so it isn't unusual that everyone in the city doesn't recognize her. If anyone disagrees with one or both of these conclusions, I hope at least the passages and analysis were useful and provided some hints as to where to look for more information.