toy rotation is great to help hams not get bored, but it can stress some hams, so try switching one toy every cage clean out to start with, and see how she gets on.
If the tubes don't serve a purpose i would personally remove them, and not look back, but if removing them means blocking off an additional space etc then possibly try giving lots of other cubby/hidey type areas including maybe a chube (big cardboard tube) with some bedding that smells like her in each to encourage her to use a different sleep area.
Good luck