Does the Quarian "history lesson" change if I've seen Tali unmasked?
Solution 1:
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."
Solution 2:
Short answer: No.
Long answer: This is apparently a fairly significant plot hole. If you romance Tali in Mass Effect 2, Shepard does remove Tali's mask. Her face is Not shown to the player, but Shepard should at least have a general idea of Quarian anatomy by the time he views these memories. However, despite having seen Tali in the nude (face and all), these memories that are being constructed are still in the full suits and masks.
Having seen her face in Mass Effect 2 has no relevance to these scenes.
Solution 3:
I romanced Tali in both Mass Effect 2 and 3, and during this mission the Quarians were masked.
At one point, Shepard asked why they were wearing masks, and the response was that these images were created based on Shepard's memories. Shepard asks if he has ever seen an unmasked Quarian, and he responds with "yes, 1" (or something similar). Shepard is then told that since he has only seen 1 Quarian that can't be used in general to show unmasked Quarians.