Maybe later Bluray releases removed them? I have an early BD release that I just watched to confirm (that line's at the 5:31 mark), and that line is present.
As for why, Tina Fey is on record regretting some of the racially insensitive jokes they made (Jenna in blackface was a big one), so maybe that was on the list? I think I've read that the Amazon streams are also edited.
Here's the article about the blackface regrets: https://people.com/tv/tina-fey-requests-removal-of-30-rock-episodes-with-blackface/
This episode wasn't mentioned, so I guess I don't know why that particular line would have been cut out.