I figured Cloud did go see his mom, but he was ashamed he never made it into SOLDIER which is why he was uncomfortable about it.
Just after getting the Huge Materia from the Rocket, I talked to Cait Sith on the bridge and he said he had told Elmyra and Marlene about Aeris' death, so it seems that you're correct.
I'm currently replaying with a different hack, and there's some seriously hard fights in there but it's great fun. I've also started to try to keep people in 'classes' of a sort, but given only three characters it can be a bit tricky to ensure you've got everything you need.
Lost Wing.