Any particular sites/webapps you like as examples of hierarchical design? I am a tech lead and struggle to come up with anything better than Material Design's nav drawers with sub-items, or equivalent.
Not the OP, but one thing that springs to mind when talking UIs and web/native is the use of breadcrumbs online. For example, if seeing a list of all other notes in the same folder isn't a key use case, an alternative could be to hide that list but make it visible when activating the list's parent. This reduces the noise so the individual note can be focussed on.
Having said that, I suspect the use cases of notes are quite varied, so a one-size-fits-all approach might not be straightforward.
Having said that, I suspect the use cases of notes are quite varied, so a one-size-fits-all approach might not be straightforward.