During a particular mission on Rannoch, I found myself viewing certain historical videos from earlier in Quarian history.
After viewing one of the videos, Shepard remarks that, given the age of the video, the Quarians should have not been wearing masks. However, I was told by my guide that the video was being drawn from my mind, and I couldn’t know what Quarians looked like under the masks since I’d never seen one without it.
However, I believe it’s possible to see Tali without her mask on in some iteration of the Mass Effect series. If I had seen Tali without her mask, would this sequence have been different?
Adding my own answer since none of the others feel entirely correct to me 😉
Playing through the game with my own ME2 save where I romanced Tali, the scene still played out as you described (with masked Quarians). I however contend that this is NOT a plot hole : Shepard commented upon this fact, with his guide (Legion, in my case) asking if he had ever seen a Quarian without his mask.
When I answered that I had indeed seen one Quarian unmasked, Legion replied with something along the lines of “then you must not associate that Quarian with the ones you are seeing”. According to Murgatroid99 in the comments below, the line is something close to : “Then your memories of that Quarian do not map to our historical data”.
This could, as Adeese mentions in his answer, mean that one Quarian is not enough to extrapolate a face for “any Quarian”; personally, though, I took it to mean that you thought well enough of Tali that you did not associate her with the Quarians willing to commit genocide on the Geth. I also like Ben Brocka’s theory in the comments to this question : “It’s how Shepard thinks of the Quarians, which is still surely painted by the dozens of suited Quarians, not the one he’s seen unmasked.”