Hi!
At the moment, no, the models uploaded to the cloud won’t save notes: they are fully read-only once uploaded. It might be possible for us to change that, but there are questions to resolve first (e.g. should anyone with the URL be able to edit and erase any notes? Should there be a way to reset the notes, and should anyone viewing the model be able to do that? Should there be a way to download the modified notes back into a Sketchup file? Maybe we should consider the option to make the uploaded models fully editable?)
There are alternatives right now: if you edit a model directly from Sketchup instead of using the “Upload model to cloud” option, then the notes, like other edits you make, are stored inside your Sketchup model. Additionally, with the experimental mode available on standalone Quest headsets, you can take a model sent from Sketchup and save a copy of it locally on the headset. This severs the connection to Sketchup, but the local file can be edited locally, including notes.