They may not have known about the Room of Requirement
It seems that Dumbledore was not aware of the Room of Requirement, or at least of how it worked. In Chapter Twenty Three of Goblet of Fire we find the following:
“Oh I would never dream of assuming I know all Hogwarts’ secrets, Igor,” said Dumbledore amicably. “Only this morning, for instance, I took a wrong turning on the way to the bathroom and found myself in a beautifully proportioned room I have never seen before, containing a really rather magnificent collection of chamber pots. When I went back to investigate more closely, I discovered that the room had vanished. But I must keep an eye out for it. Possibly it is only accessible at five-thirty in the morning. Or it may only appear at the quarter moon — or when the seeker has an exceptionally full bladder.”
In Chapter Eighteen of Order of the Phoenix Harry thinks of this when Dobby explains the Room of Requirement to him, indicating that Dumbledore may not have been aware of the room's true abilities:
“— and if you really needed a bathroom,” said Harry, suddenly remembering something Dumbledore had said at the Yule Ball the previous Christmas, “would it fill itself with chamber pots?”
In Chapter Twenty-One of Half-Blood Prince, faced with the fact that the room does not appear on the Marauder's Map, Ron suggests that its creators were unaware of the room's existence:
“The Room of Requirement!” said Harry, smacking himself hard on the forehead with Advanced Potion-Making. Hermione and Ron stared at him. “That’s where he’s been sneaking off to! That’s where he’s doing... whatever he’s doing! And I bet that’s why he’s been disappearing off the map — come to think of it, I’ve never seen the Room of Requirement on there!”
“Maybe the Marauders never knew the room was there,” said Ron.
And even if they were aware of the room, they presumably only became aware of it long after the Whomping Willow arrangement had been set up. In Chapter Eighteen of Prisoner of Azkaban we find the following:
I’m getting there, Sirius, I’m getting there... well, highly exciting possibilities were open to us now that we could all transform. Soon we were leaving the Shrieking Shack and roaming the school grounds and the village by night. Sirius and James transformed into such large animals, they were able to keep a werewolf in check. I doubt whether any Hogwarts students ever found out more about the Hogwarts grounds and Hogsmeade than we did.... And that’s how we came to write the Marauder’s Map, and sign it with our nicknames. Sirius is Padfoot. Peter is Wormtail. James was Prongs.”
It seems clear from here that the bulk of their knowledge of the castle came from their excursions as animagi, which moments earlier Lupin had said did not occur until their fifth year:
“Yes, indeed,” said Lupin. “It took them the best part of three years to work out how to do it. Your father and Sirius here were the cleverest students in the school, and lucky they were, because the Animagus transformation can go horribly wrong — one reason the Ministry keeps a close watch on those attempting to do it. Peter needed all the help he could get from James and Sirius. Finally, in our fifth year, they managed it. They could each turn into a different animal at will.”
And once they did discover the Room of Requirement (if they did) they would be unlikely to tell the administration about it and suggest it for Lupin's use, particularly if it might raise awkward questions.
