Hi and congratulations on the unexpected new arrivals.
What sort of hamster is Waffles?! If she's a Syrian - the biggest sort of hamster - a Crittertrail cage isn't suitable for her at all, babies or no babies, as it just doesn't give the correct amount of floor space.
I would imagine that a Crittertrail could be very dangerous for babies - they could get trapped in the tubes, dropped down them etc and the height of a Crittertrail 2 could also be a big risk. Plus the bars would be wide enough for a baby to crawl out of.....
It's a difficult one to make suggestions on as if you disturb the nest she may kill the babies anyway through stress. I think if you could possibly move the whole petting zone (thing at the top) into a new cage such as a Zoozone 1 / Gabber Rex (all on one level) and make sure you put her old bedding / substrate in there too this may be an option for you - but I've never had a hamster with babies so I'm not sure what to suggest.
Perhaps it may be best at the moment to keep an eye on her and when the babies are moving around more move them into a safer cage as you are already considering? Wish I had more definite help for you but it's a difficult one to weigh up.
Whereabouts are you located? Someone may have a safer cage they can lend you for the babies.
Is she from a pet shop? If she is, and they sold you a pregnant hamster, you could certainly ask them for a free safe 'cage' (needs to be an enclosed one without bars like a Rody / Duna / Zoozone or a tank though you need to check the bar spacing on the top) for her to raise her litter in as this is their mistake. *Don't* hand her over with the babies though if they suggest it, I'm sure the babies will be better off with you!
ETA: Aha! Just read Souffles' suggestions in your duplicate post in B+V. It seems that she agrees that in this case the risk of danger to the babies in the cage they are in is greater than the risk of stressing Waffles out. I would go with this advice.