It is never clearly stated in the movie if the others knew about the rape, although we can be sure that they knew that whatever Noodles did, did not go well.
When Noodles comes back to his partners, he tries to act casually by mocking Max who's sitting on a throne. But all around him faces are cautious and gloomy, and nobody dares to speak a word except for Max who accuses Noodles of taking "a vacation" while the others are working and earning big money and don't put "broads in the way of business".
The atmosphere of the whole scene is beautifully captured by the seemingly endless coffee stirring of Noodles, and the tension is only loosened after Max's joke about his "way with women", which follows his almost literally kicking away his girlfriend Carol from the room, thus demonstrating to Noodles and everyone else that his priority is business and that girls are disposable.
We can only speculate about the sometimes awkward, sometimes tense glances between Moe and Noodles as the latter asks the first if there's still coffee around or if Noodles, after seeing Moe standing behind him with a pair of scissors and a paper clipping, is wondering whether Moe is taking care of the gang's diary or if he's going to plunge those scissors in his neck.
We don't even know for sure how long Noodles has been away.
In the recently released extended version of the movie, which contains 26 minutes of previously unreleased footage, after the rape scene in which we see Noodles abandoned at dawn by the driver on a desert road, he goes to the speakeasy where he gets drunk, meets Eve and then spends the night with her trying to forget Deborah. The morning after he wakes up alone and then goes to the train station, only to watch Deborah's train departing from the station.
However, when Noodles returns to the gang and replies to the accuses of disappearing by saying that they could have looked for him, Max says that they did and that Cockeye found him "at the Chink's, so doped up that he didn't even recognize him". "You called me Deborah", mockingly adds Cockeye.
Anyway, while this uncertainty about the accountability, so to speak, of Noodles whereabouts might be ascribed to editing problems (according to Wikipedia Leone accumulated something like 10 hours of footage), my opinion is that the rest, not differently to other more important parts of the movie, is intentionally left to the viewer's interpretation by Leone.
Here's part of the scene: