<But wouldn't they have noticed the ice clump formation , even without the RMS?

I guess it depends on whether the water dump port was visible from the crew compartment. How visible would it be with the SpaceHab module in the cargo bay? This part of the STS-41 entry suggests to me that the port isn't always visible.

There also were indications that ice had formed around the waste water dump nozzle, but it was believed that the ice did not remain. The RMS (remote manipulator system) was deployed and the RMS TV showed a large column of ice over the supply nozzle.

It sounds like they couldn't see the ice on that flight without the RMS, and we know Columbia wasn't carrying the RMS on this mission.